9XU3 image
Deposition Date 2025-11-24
Release Date 2026-08-12
Last Version Date 2026-08-12
Entry Detail
PDB ID:
9XU3
Keywords:
SPLICING
Title:
Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9XU3 validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:MSE-U12_5 exon
Chain IDs:A (auth: 0)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:MSE-U12_intron-3 exon
Chain IDs:B (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U12 snRNA
Chain IDs:C (auth: 2)
Chain Length:0
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:0
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:0
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U6atac snRNA
Chain IDs:F (auth: 6)
Chain Length:0
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:0
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:0
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:0
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:0
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:0
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:0
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:0
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:0
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:0
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:0
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:0
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:0
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:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM2
Chain IDs:S (auth: L2)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y333 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM3
Chain IDs:T (auth: L3)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62310 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM4
Chain IDs:U (auth: L4)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y4Z0 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM5
Chain IDs:V (auth: L5)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y4Y9 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM6
Chain IDs:W (auth: L6)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62312 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM7
Chain IDs:X (auth: L7)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UK45 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM8
Chain IDs:Y (auth: L8)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O95777 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Armadillo repeat-containing p
Gene (Uniprot):ARMC7
Chain IDs:Z (auth: M)
Chain Length:0
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:AA (auth: N)
Chain Length:0
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:BA (auth: O)
Chain Length:0
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:CA (auth: P)
Chain Length:0
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:DA (auth: Q)
Chain Length:0
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:Peptidyl-prolyl cis-trans iso
Gene (Uniprot):PPIL3
Chain IDs:EA (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H2H8 Pfam ID:PF00160 EC:5.2.1.8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SLU7
Gene (Uniprot):SLU7
Chain IDs:FA (auth: S)
Chain Length:0
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:ATP-dependent RNA helicase DH
Gene (Uniprot):DHX8
Chain IDs:GA (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14562 Pfam ID:PF00575, 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:HA (auth: U)
Chain Length:0
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:IA (auth: V)
Chain Length:0
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:WD repeat-containing protein
Gene (Uniprot):WDR25
Chain IDs:JA (auth: W)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q64LD2 Pfam ID:PF00400
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor Cactin
Gene (Uniprot):CACTIN
Chain IDs:KA (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WUQ7 Pfam ID:PF10312, PF09732
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein FAM32A
Gene (Uniprot):FAM32A
Chain IDs:LA (auth: Y)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y421 Pfam ID:PF08555
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:NF-kappa-B-activating protein
Gene (Uniprot):NKAP
Chain IDs:MA (auth: Z)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N5F7 Pfam ID:PF15692, PF06047
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPB
Chain IDs:NA (auth: a), UA (auth: h)
Chain Length:0
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:OA (auth: b), VA (auth: i)
Chain Length:0
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:PA (auth: c), WA (auth: j)
Chain Length:0
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:QA (auth: d), XA (auth: k)
Chain Length:0
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:RA (auth: e), YA (auth: l)
Chain Length:0
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:SA (auth: f), ZA (auth: m)
Chain Length:0
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:TA (auth: g), AB (auth: n)
Chain Length:0
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:Splicing factor ESS-2 homolog
Gene (Uniprot):ESS2
Chain IDs:BB (auth: p)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DF8 Pfam ID:PF09751
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 19
Gene (Uniprot):PRPF19
Chain IDs:CB (auth: q), DB (auth: r), EB (auth: s), FB (auth: t)
Chain Length:0
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:GB (auth: u)
Chain Length:0
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:HB (auth: v)
Chain Length:0
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:IB (auth: w)
Chain Length:0
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:JB (auth: x)
Chain Length:0
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:RNA-binding protein 41
Gene (Uniprot):RBM41
Chain IDs:KB (auth: y)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96IZ5 Pfam ID:PF00076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein FAM204A
Gene (Uniprot):FAM204A
Chain IDs:LB (auth: z)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H8W3
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP P SER modified residue
Ligand Molecules
ADP
ATP
GTP
IHP
K
MG
ZN
Primary Citation
Molecular mechanism of the catalysis for U12-type splicing by the human
Vita ? ? ? (2026)
DOI: 10.15302/vita.2026.06.0042
Primary Citation of related structures
9XU3
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