9XU3 | pdb_00009xu3

Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)

  • Classification: SPLICING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-11-24 Released: 2026-08-12 
  • Deposition Author(s): Wan, R., Bai, R.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XU3

This is version 1.0 of the entry. See complete history. 

Literature

Molecular mechanism of the catalysis for U12-type splicing by the human

Bai, R., Guo, H., Sun, R., Zhu, Y., Shi, Y., Wan, R.

(2026) Vita 

Macromolecule Content 

  • Total Structure Weight: 3,323.39 kDa 
  • Atom Count: 123,688 
  • Modeled Residue Count: 16,694 
  • Deposited Residue Count: 27,894 
  • Unique protein chains: 49
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidylprolyl isomerase domain and WD repeat-containing protein 1D [auth 4]646Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q96BP3 (Homo sapiens)
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GTEx:  ENSG00000113593 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8G [auth A]2,335Homo sapiensMutation(s): 0 
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Find proteins for Q6P2Q9 (Homo sapiens)
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GTEx:  ENSG00000174231 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentH [auth B]972Homo sapiensMutation(s): 0 
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Find proteins for Q15029 (Homo sapiens)
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GTEx:  ENSG00000108883 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseI [auth C]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O75643 (Homo sapiens)
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GTEx:  ENSG00000144028 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinJ [auth D]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinK [auth E]802Homo sapiensMutation(s): 0 
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Find proteins for Q99459 (Homo sapiens)
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GTEx:  ENSG00000096401 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1L [auth F]855Homo sapiensMutation(s): 0 
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Find proteins for Q9HCS7 (Homo sapiens)
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GTEx:  ENSG00000076924 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1M [auth G]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 12N [auth H]166Homo sapiensMutation(s): 0 
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Find proteins for Q8WUD4 (Homo sapiens)
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GTEx:  ENSG00000160799 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologO [auth I]285Homo sapiensMutation(s): 0 
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Find proteins for Q9ULR0 (Homo sapiens)
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GTEx:  ENSG00000240682 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1P [auth J]536Homo sapiensMutation(s): 0 
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Find proteins for Q13573 (Homo sapiens)
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GTEx:  ENSG00000100603 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1Q [auth K]514Homo sapiensMutation(s): 0 
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Find proteins for O43660 (Homo sapiens)
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GTEx:  ENSG00000171566 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding protein 48R [auth L]367Homo sapiensMutation(s): 0 
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Find proteins for Q5RL73 (Homo sapiens)
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GTEx:  ENSG00000127993 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2S [auth L2]95Homo sapiensMutation(s): 0 
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Find proteins for Q9Y333 (Homo sapiens)
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GTEx:  ENSG00000204392 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3T [auth L3]102Homo sapiensMutation(s): 0 
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Find proteins for P62310 (Homo sapiens)
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GTEx:  ENSG00000170860 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4U [auth L4]139Homo sapiensMutation(s): 0 
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Find proteins for Q9Y4Z0 (Homo sapiens)
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GTEx:  ENSG00000130520 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5V [auth L5]91Homo sapiensMutation(s): 0 
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Find proteins for Q9Y4Y9 (Homo sapiens)
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GTEx:  ENSG00000106355 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6W [auth L6]80Homo sapiensMutation(s): 0 
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Find proteins for P62312 (Homo sapiens)
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GTEx:  ENSG00000164167 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7X [auth L7]103Homo sapiensMutation(s): 0 
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Find proteins for Q9UK45 (Homo sapiens)
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GTEx:  ENSG00000130332 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8Y [auth L8]96Homo sapiensMutation(s): 0 
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Find proteins for O95777 (Homo sapiens)
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GTEx:  ENSG00000128534 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Armadillo repeat-containing protein 7Z [auth M]198Homo sapiensMutation(s): 0 
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Find proteins for Q9H6L4 (Homo sapiens)
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GTEx:  ENSG00000125449 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologAA [auth N]229Homo sapiensMutation(s): 0 
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Find proteins for Q9P013 (Homo sapiens)
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GTEx:  ENSG00000150316 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1BA [auth O]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9Y3C6 (Homo sapiens)
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GTEx:  ENSG00000137168 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase ECA [auth P]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9UNP9 (Homo sapiens)
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GTEx:  ENSG00000084072 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA helicase aquariusDA [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O60306 (Homo sapiens)
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GTEx:  ENSG00000021776 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 3EA [auth R]161Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9H2H8 (Homo sapiens)
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GTEx:  ENSG00000240344 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7FA [auth S]586Homo sapiensMutation(s): 0 
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Find proteins for O95391 (Homo sapiens)
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GTEx:  ENSG00000164609 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8GA [auth T]1,220Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for Q14562 (Homo sapiens)
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GTEx:  ENSG00000067596 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2HA [auth U]2,752Homo sapiensMutation(s): 0 
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Find proteins for Q9UQ35 (Homo sapiens)
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GTEx:  ENSG00000167978 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologIA [auth V]908Homo sapiensMutation(s): 0 
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Find proteins for Q9HCG8 (Homo sapiens)
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GTEx:  ENSG00000163510 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 25JA [auth W]544Homo sapiensMutation(s): 0 
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Find proteins for Q64LD2 (Homo sapiens)
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GTEx:  ENSG00000176473 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor CactinKA [auth X]758Homo sapiensMutation(s): 0 
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Find proteins for Q8WUQ7 (Homo sapiens)
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GTEx:  ENSG00000105298 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein FAM32ALA [auth Y]112Homo sapiensMutation(s): 0 
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Find proteins for Q9Y421 (Homo sapiens)
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GTEx:  ENSG00000105058 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
NF-kappa-B-activating proteinMA [auth Z]415Homo sapiensMutation(s): 0 
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Find proteins for Q8N5F7 (Homo sapiens)
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GTEx:  ENSG00000101882 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'NA [auth a],
UA [auth h]		240Homo sapiensMutation(s): 0 
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Find proteins for P14678 (Homo sapiens)
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GTEx:  ENSG00000125835 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1OA [auth b],
VA [auth i]		119Homo sapiensMutation(s): 0 
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Find proteins for P62314 (Homo sapiens)
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GTEx:  ENSG00000167088 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2PA [auth c],
WA [auth j]		118Homo sapiensMutation(s): 0 
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Find proteins for P62316 (Homo sapiens)
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GTEx:  ENSG00000125743 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3QA [auth d],
XA [auth k]		126Homo sapiensMutation(s): 0 
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Find proteins for P62318 (Homo sapiens)
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GTEx:  ENSG00000100028 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ERA [auth e],
YA [auth l]		92Homo sapiensMutation(s): 0 
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Find proteins for P62304 (Homo sapiens)
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GTEx:  ENSG00000182004 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FSA [auth f],
ZA [auth m]		86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GAB [auth n],
TA [auth g]		76Homo sapiensMutation(s): 0 
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Find proteins for P62308 (Homo sapiens)
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GTEx:  ENSG00000143977 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor ESS-2 homologBB [auth p]476Homo sapiensMutation(s): 0 
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Find proteins for Q96DF8 (Homo sapiens)
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GTEx:  ENSG00000100056 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19CB [auth q],
DB [auth r],
EB [auth s],
FB [auth t]		504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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Find proteins for Q9UMS4 (Homo sapiens)
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GTEx:  ENSG00000110107 
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UniProt GroupQ9UMS4
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Reference Sequence
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27GB [auth u]225Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75934 (Homo sapiens)
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Go to UniProtKB:  O75934
GTEx:  ENSG00000116752 
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UniProt GroupO75934
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIHB [auth v]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P38919 (Homo sapiens)
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GTEx:  ENSG00000141543 
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UniProt GroupP38919
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein mago nashi homologIB [auth w]146Homo sapiensMutation(s): 0 
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Find proteins for P61326 (Homo sapiens)
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GTEx:  ENSG00000162385 
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UniProt GroupP61326
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding protein 8AJB [auth x]174Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5S9 (Homo sapiens)
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GTEx:  ENSG00000265241 
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UniProt GroupQ9Y5S9
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding protein 41KB [auth y]413Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96IZ5 (Homo sapiens)
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Go to UniProtKB:  Q96IZ5
GTEx:  ENSG00000089682 
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UniProt GroupQ96IZ5
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein FAM204ALB [auth z]233Homo sapiensMutation(s): 0 
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Find proteins for Q9H8W3 (Homo sapiens)
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GTEx:  ENSG00000165669 
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UniProt GroupQ9H8W3
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Entity ID: 1
MoleculeChains LengthOrganismImage
MSE-U12_5 exonA [auth 0]57Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
MSE-U12_intron-3 exonB [auth 1]277Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
U12 snRNAC [auth 2]150Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
U5 snRNAE [auth 5]117Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
U6atac snRNAF [auth 6]125Homo sapiens
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
(Subject of Investigation/LOI)

Query on IHP


Download:Ideal Coordinates CCD File
UB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
(Subject of Investigation/LOI)

Query on GTP


Download:Ideal Coordinates CCD File
VB [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
(Subject of Investigation/LOI)

Query on ATP


Download:Ideal Coordinates CCD File
CC [auth v]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP


Download:Ideal Coordinates CCD File
XB [auth C],
YB [auth C]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN


Download:Ideal Coordinates CCD File
AC [auth S]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
(Subject of Investigation/LOI)

Query on K


Download:Ideal Coordinates CCD File
SB [auth 6],
TB [auth 6]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG


Download:Ideal Coordinates CCD File
BC [auth v]
MB [auth 1]
NB [auth 1]
OB [auth 6]
PB [auth 6]
BC [auth v],
MB [auth 1],
NB [auth 1],
OB [auth 6],
PB [auth 6],
QB [auth 6],
RB [auth 6],
WB [auth B],
ZB [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		P [auth J]L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171214

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release