ISDA: 9XTT

Deposition Date 2025-11-23

Release Date 2026-08-12

Last Version Date 2026-08-12

Entry Detail

PDB ID:

9XTT

Keywords:

SPLICING

Title:

Human minor spliceosome branching-completed C complex (after step-I)

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Saccharomyces cerevisiae

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.92 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:MSE-U12_exon
Chain IDs:A (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:MSE-U12_Intron
Chain IDs:B (auth: 1)
Chain Length:277
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:U12 snRNA
Chain IDs:C (auth: 2)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidylprolyl isomerase doma
Gene (Uniprot):PPWD1
Chain IDs:D (auth: 4)
Chain Length:646
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96BP3 Pfam ID:PF00400, PF00160 EC:5.2.1.8

Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:E (auth: 5)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:U6atac snRNA
Chain IDs:F (auth: 6)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing-splicing
Gene (Uniprot):PRPF8
Chain IDs:G (auth: A)
Chain Length:2335
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6P2Q9 Pfam ID:PF08082, PF08083, PF10598, PF10597, PF10596, PF12134, PF01398, PF08084

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:116 kDa U5 small nuclear ribo
Gene (Uniprot):EFTUD2
Chain IDs:H (auth: B)
Chain Length:972
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15029 Pfam ID:PF16004, PF00009, PF03144, PF14492, PF03764, PF00679

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleopr
Gene (Uniprot):SNRNP200
Chain IDs:I (auth: C)
Chain Length:2136
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75643 Pfam ID:PF21188, PF18149, PF00270, PF00271, PF23445, PF02889 EC:3.6.4.13

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleopr
Gene (Uniprot):SNRNP40
Chain IDs:J (auth: D)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96DI7 Pfam ID:PF00400

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cell division cycle 5-like pr
Gene (Uniprot):CDC5L
Chain IDs:K (auth: E)
Chain Length:802
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q99459 Pfam ID:PF13921, PF11831

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SYF1
Gene (Uniprot):XAB2
Chain IDs:L (auth: F)
Chain Length:855
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9HCS7 Pfam ID:PF23233, PF23220, PF23231

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Crooked neck-like protein 1
Gene (Uniprot):CRNKL1
Chain IDs:M (auth: G)
Chain Length:848
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BZJ0 Pfam ID:PF23231

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing
Gene (Uniprot):CCDC12
Chain IDs:N (auth: H)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8WUD4 Pfam ID:PF08315

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor ISY1
Gene (Uniprot):ISY1
Chain IDs:O (auth: I)
Chain Length:285
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9ULR0 Pfam ID:PF06246

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:SNW domain-containing protein
Gene (Uniprot):SNW1
Chain IDs:P (auth: J)
Chain Length:536
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13573 Pfam ID:PF02731

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pleiotropic regulator 1
Gene (Uniprot):PLRG1
Chain IDs:Q (auth: K)
Chain Length:514
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O43660 Pfam ID:PF00400

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA-binding protein 48
Gene (Uniprot):RBM48
Chain IDs:R (auth: L)
Chain Length:367
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q5RL73

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Armadillo repeat-containing p
Gene (Uniprot):ARMC7
Chain IDs:S (auth: M)
Chain Length:198
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H6L4 Pfam ID:PF00514

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spliceosome-associated protei
Gene (Uniprot):CWC15
Chain IDs:T (auth: N)
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P013 Pfam ID:PF04889

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans iso
Gene (Uniprot):PPIL1
Chain IDs:U (auth: O)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3C6 Pfam ID:PF00160 EC:5.2.1.8

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans iso
Gene (Uniprot):PPIE
Chain IDs:V (auth: P)
Chain Length:301
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UNP9 Pfam ID:PF00076, PF00160 EC:5.2.1.8

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA helicase aquarius
Gene (Uniprot):AQR
Chain IDs:W (auth: Q)
Chain Length:1485
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O60306 Pfam ID:PF16399, PF21143, PF21144, PF13086, PF13087 EC:3.6.4.13

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC2
Gene (Uniprot):CWC25
Chain IDs:X (auth: R)
Chain Length:425
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NXE8 Pfam ID:PF10197, PF12542

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SLU7
Gene (Uniprot):SLU7
Chain IDs:Y (auth: S)
Chain Length:586
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O95391 Pfam ID:PF11708

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor ATP-
Gene (Uniprot):DHX38
Chain IDs:Z (auth: T)
Chain Length:1227
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q92620 Pfam ID:PF00270, PF00271, PF04408, PF21010, PF07717 EC:3.6.4.13

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Serine/arginine repetitive ma
Gene (Uniprot):SRRM2
Chain IDs:AA (auth: U)
Chain Length:2752
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UQ35 Pfam ID:PF08312

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC2
Gene (Uniprot):CWC22
Chain IDs:BA (auth: V)
Chain Length:908
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9HCG8 Pfam ID:PF02854, PF02847

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein FRG1
Gene (Uniprot):FRG1
Chain IDs:CA (auth: X)
Chain Length:258
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q14331 Pfam ID:PF06229

Polymer Type:polypeptide(L)
Molecule:Unknown polymer
Chain IDs:DA (auth: X1)
Chain Length:20
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Unknown polymer
Chain IDs:EA (auth: X2)
Chain Length:18
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Unknown polymer
Chain IDs:FA (auth: X3)
Chain Length:21
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor YJU2
Gene (Uniprot):YJU2
Chain IDs:GA (auth: Y)
Chain Length:345
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BW85 Pfam ID:PF04502

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein
Gene (Uniprot):WDR70
Chain IDs:HA (auth: Z)
Chain Length:654
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NW82 Pfam ID:PF00400

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPB
Chain IDs:IA (auth: a), PA (auth: h)
Chain Length:240
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P14678 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPD1
Chain IDs:JA (auth: b), QA (auth: i)
Chain Length:119
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62314 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPD2
Chain IDs:KA (auth: c), RA (auth: j)
Chain Length:118
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62316 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPD3
Chain IDs:LA (auth: d), SA (auth: k)
Chain Length:126
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62318 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPE
Chain IDs:MA (auth: e), TA (auth: l)
Chain Length:92
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62304 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPF
Chain IDs:NA (auth: f), UA (auth: m)
Chain Length:86
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62306 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPG
Chain IDs:OA (auth: g), VA (auth: n)
Chain Length:76
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62308 Pfam ID:PF01423

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 19
Gene (Uniprot):PRPF19
Chain IDs:WA (auth: q), XA (auth: r), YA (auth: s), ZA (auth: t)
Chain Length:504
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:Q9UMS4 Pfam ID:PF04564, PF08606, PF24814 EC:2.3.2.27

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SPF2
Gene (Uniprot):BCAS2
Chain IDs:AB (auth: u)
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75934 Pfam ID:PF05700

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic initiation factor
Gene (Uniprot):EIF4A3
Chain IDs:BB (auth: v)
Chain Length:411
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P38919 Pfam ID:PF00270, PF00271 EC:3.6.4.13

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein mago nashi homolog
Gene (Uniprot):MAGOH
Chain IDs:CB (auth: w)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61326 Pfam ID:PF02792

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA-binding protein 8A
Gene (Uniprot):RBM8A
Chain IDs:DB (auth: x)
Chain Length:174
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y5S9 Pfam ID:PF00076

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Multiple myeloma tumor-associ
Gene (Uniprot):MMTAG2
Chain IDs:EB (auth: z)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BU76 Pfam ID:PF10159

Modified Residue