9PDK image
Deposition Date 2025-06-30
Release Date 2026-10-14
Last Version Date 2026-10-14
Entry Detail
PDB ID:
9PDK
Keywords:
TRANSCRIPTION
Title:
Composite map of closed form of PIC-Med-SWI/SNF
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae (Taxon ID: 4932)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9PDK validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):RAD3
Chain IDs:A (auth: B0), KB (auth: A0)
Chain Length:778
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06839 EC:5.6.2.3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB1
Chain IDs:B (auth: B1), LB (auth: A1)
Chain Length:642
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32776
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB2
Chain IDs:C (auth: B2), MB (auth: A2)
Chain Length:513
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02939
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II transcripti
Gene (Uniprot):TFB3
Chain IDs:D (auth: B3), NB (auth: A3)
Chain Length:321
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q03290
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB4
Chain IDs:E (auth: B4), OB (auth: A4)
Chain Length:338
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12004
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB5
Chain IDs:F (auth: B5), PB (auth: A5)
Chain Length:72
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7C1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):SSL1
Chain IDs:G (auth: B6), QB (auth: A6)
Chain Length:461
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04673
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):SSL2
Chain IDs:H (auth: B7), RB (auth: A7)
Chain Length:843
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q00578 EC:3.6.4.12
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:SWI/SNF chromatin-remodeling
Gene (Uniprot):SNF5
Chain IDs:I (auth: B8), DB (auth: sF), SB (auth: A8), ND (auth: SF)
Chain Length:905
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae
UniProt ID:P18480
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TAF14
Chain IDs:J (auth: B9), TB (auth: A9)
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35189
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPO21
Chain IDs:K (auth: BA), HA (auth: mA), UB (auth: AA), RC (auth: MA)
Chain Length:1733
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04050 EC:2.7.7.6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB2
Chain IDs:L (auth: BB), VB (auth: AB)
Chain Length:1224
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P08518 EC:2.7.7.6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB3
Chain IDs:M (auth: BC), WB (auth: AC)
Chain Length:318
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P16370
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB4
Chain IDs:N (auth: BD), XB (auth: AD)
Chain Length:221
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20433
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPB5
Chain IDs:O (auth: BE), YB (auth: AE)
Chain Length:215
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20434
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPO26
Chain IDs:P (auth: BF), ZB (auth: AF)
Chain Length:155
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20435
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB7
Chain IDs:Q (auth: BG), AC (auth: AG)
Chain Length:171
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P34087
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPB8
Chain IDs:R (auth: BH), BC (auth: AH)
Chain Length:146
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20436
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB9
Chain IDs:S (auth: BI), CC (auth: AI)
Chain Length:122
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P27999
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPB10
Chain IDs:T (auth: BJ), DC (auth: AJ)
Chain Length:70
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22139
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB11
Chain IDs:U (auth: BK), EC (auth: AK)
Chain Length:120
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38902
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPC10
Chain IDs:V (auth: BL), FC (auth: AL)
Chain Length:70
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40422
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):SUA7
Chain IDs:W (auth: BM), GC (auth: AM)
Chain Length:345
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P29055
Polymer Type:polydeoxyribonucleotide
Molecule:promoter DNA
Chain IDs:X (auth: BN), HC (auth: AN)
Chain Length:69
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):SPT15
Chain IDs:Y (auth: BO), IC (auth: AO)
Chain Length:240
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P13393
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFG1
Chain IDs:Z (auth: BQ), JC (auth: AQ)
Chain Length:735
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41895
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFG2
Chain IDs:AA (auth: BR), KC (auth: AR)
Chain Length:400
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41896
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation fact
Gene (Uniprot):DST1
Chain IDs:BA (auth: BS), LC (auth: AS)
Chain Length:309
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07273
Polymer Type:polydeoxyribonucleotide
Molecule:promoter DNA
Chain IDs:CA (auth: BT), MC (auth: AT)
Chain Length:69
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TOA1
Chain IDs:DA (auth: BU), NC (auth: AU)
Chain Length:286
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32773
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TOA2
Chain IDs:EA (auth: BV), OC (auth: AV)
Chain Length:122
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32774
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFA1
Chain IDs:FA (auth: BW), PC (auth: AW)
Chain Length:482
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36100
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFA2
Chain IDs:GA (auth: BX), QC (auth: AX)
Chain Length:328
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36145
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED2
Chain IDs:UD (auth: T1), AE (auth: t1)
Chain Length:431
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12124
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):PGD1
Chain IDs:VD (auth: T2), BE (auth: t2)
Chain Length:397
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40356
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):NUT1
Chain IDs:WD (auth: T3), CE (auth: t3)
Chain Length:1132
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53114 EC:2.3.1.48
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):GAL11
Chain IDs:YD (auth: T5), EE (auth: t5)
Chain Length:1081
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P19659
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SIN4
Chain IDs:ZD (auth: T6), FE (auth: t6)
Chain Length:974
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32259
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED6
Chain IDs:IA (auth: ma), SC (auth: Ma)
Chain Length:295
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38782
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED8
Chain IDs:JA (auth: mb), TC (auth: Mb)
Chain Length:223
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38304
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED11
Chain IDs:KA (auth: mc), UC (auth: Mc)
Chain Length:115
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q99278
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SRB4
Chain IDs:LA (auth: md), VC (auth: Md)
Chain Length:687
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32569
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SRB5
Chain IDs:MA (auth: me), WC (auth: Me)
Chain Length:307
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32585
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SRB2
Chain IDs:NA (auth: mf), XC (auth: Mf)
Chain Length:210
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P34162
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SRB6
Chain IDs:OA (auth: mg), YC (auth: Mg)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32570
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED4
Chain IDs:PA (auth: mh), ZC (auth: Mh)
Chain Length:284
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12343
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED7
Chain IDs:QA (auth: mi), AD (auth: Mi)
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08278
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):CSE2
Chain IDs:RA (auth: mj), BD (auth: Mj)
Chain Length:149
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P33308
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):NUT2
Chain IDs:SA (auth: mk), CD (auth: Mk)
Chain Length:157
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q06213
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):RGR1
Chain IDs:TA (auth: ml), DD (auth: Ml), XD (auth: T4), DE (auth: t4)
Chain Length:1082
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae
UniProt ID:P19263
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):ROX3
Chain IDs:UA (auth: mm), ED (auth: Mm)
Chain Length:220
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25046
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SRB7
Chain IDs:VA (auth: mn), FD (auth: Mn)
Chain Length:140
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P47822
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):SOH1
Chain IDs:WA (auth: mo), GD (auth: Mo)
Chain Length:127
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38633
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED1
Chain IDs:XA (auth: mp), HD (auth: Mp)
Chain Length:566
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12321
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription regulatory prot
Gene (Uniprot):SNF12
Chain IDs:YA (auth: sA), ID (auth: SA)
Chain Length:566
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53628
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:SWI/SNF complex subunit SWI3
Gene (Uniprot):SWI3
Chain IDs:ZA (auth: sB), BB (auth: sD), JD (auth: SB), LD (auth: SD)
Chain Length:825
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32591
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription regulatory prot
Gene (Uniprot):SNF6
Chain IDs:AB (auth: sC), KD (auth: SC)
Chain Length:332
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P18888
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:SWI/SNF global transcription
Gene (Uniprot):SWP82
Chain IDs:CB (auth: sE), MD (auth: SE)
Chain Length:623
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P43554
Polymer Type:polypeptide(L)
Molecule:unsigned peptide of SWISNF
Chain IDs:EB (auth: sG), OD (auth: SG)
Chain Length:47
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription regulatory prot
Gene (Uniprot):SNF2
Chain IDs:FB (auth: sH), PD (auth: SH)
Chain Length:1703
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22082 EC:3.6.4.-
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:SWI/SNF chromatin-remodeling
Gene (Uniprot):SWI1
Chain IDs:GB (auth: sI), QD (auth: SI)
Chain Length:1314
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P09547
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Regulator of Ty1 transpositio
Gene (Uniprot):RTT102
Chain IDs:HB (auth: sJ), RD (auth: SJ)
Chain Length:157
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53330
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 7
Gene (Uniprot):ARP7
Chain IDs:IB (auth: sK), SD (auth: SK)
Chain Length:477
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12406
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-like protein ARP9
Gene (Uniprot):ARP9
Chain IDs:JB (auth: sL), TD (auth: SL)
Chain Length:467
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q05123
Ligand Molecules
MG
SF4
ZN
Primary Citation
Composite map of closed form of PIC-Med-SWI/SNF
To Be Published ? ? ? (?)
Primary Citation of related structures
9PB2
9PB3
9PC8
9PB7
9PB8
9PBD
9PBI
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