9XTT | pdb_00009xtt

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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: 3,117.42 kDa 
  • Atom Count: 117,342 
  • Modeled Residue Count: 15,642 
  • Deposited Residue Count: 26,087 
  • Unique protein chains: 42
  • 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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GTEx:  ENSG00000113593 
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UniProt GroupQ96BP3
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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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PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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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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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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Find proteins for Q96DI7 (Homo sapiens)
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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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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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Find proteins for Q9BZJ0 (Homo sapiens)
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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
Armadillo repeat-containing protein 7S [auth M]198Homo sapiensMutation(s): 0 
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Find proteins for Q9H6L4 (Homo sapiens)
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PHAROS:  Q9H6L4
GTEx:  ENSG00000125449 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologT [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: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1U [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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PHAROS:  Q9Y3C6
GTEx:  ENSG00000137168 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EV [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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PHAROS:  Q9UNP9
GTEx:  ENSG00000084072 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA helicase aquariusW [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: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25 homologX [auth R]425Homo sapiensMutation(s): 0 
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Find proteins for Q9NXE8 (Homo sapiens)
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PHAROS:  Q9NXE8
GTEx:  ENSG00000273559 
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UniProt GroupQ9NXE8
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7Y [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: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16Z [auth T]1,227Homo sapiensMutation(s): 1 
Gene Names: DHX38, DDX38, KIAA0224, PRP16
EC: 3.6.4.13
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Find proteins for Q92620 (Homo sapiens)
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GTEx:  ENSG00000140829 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2AA [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: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologBA [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: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein FRG1CA [auth X]258Homo sapiensMutation(s): 0 
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Find proteins for Q14331 (Homo sapiens)
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GTEx:  ENSG00000109536 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown polymerDA [auth X1]20Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown polymerEA [auth X2]18Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown polymerFA [auth X3]21Homo sapiensMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor YJU2GA [auth Y]345Homo sapiensMutation(s): 0 
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Find proteins for Q9BW85 (Homo sapiens)
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GTEx:  ENSG00000105248 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 70HA [auth Z]654Homo sapiensMutation(s): 0 
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Find proteins for Q9NW82 (Homo sapiens)
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GTEx:  ENSG00000082068 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'IA [auth a],
PA [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: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1JA [auth b],
QA [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: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2KA [auth c],
RA [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: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3LA [auth d],
SA [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: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EMA [auth e],
TA [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: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FNA [auth f],
UA [auth m]		86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GOA [auth g],
VA [auth n]		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: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19WA [auth q],
XA [auth r],
YA [auth s],
ZA [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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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27AB [auth u]225Homo sapiensMutation(s): 0 
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Find proteins for O75934 (Homo sapiens)
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PHAROS:  O75934
GTEx:  ENSG00000116752 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIBB [auth v]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for P38919 (Homo sapiens)
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GTEx:  ENSG00000141543 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein mago nashi homologCB [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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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding protein 8ADB [auth x]174Homo sapiensMutation(s): 0 
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Find proteins for Q9Y5S9 (Homo sapiens)
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GTEx:  ENSG00000265241 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Multiple myeloma tumor-associated protein 2EB [auth z]263Homo sapiensMutation(s): 0 
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Find proteins for Q9BU76 (Homo sapiens)
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PHAROS:  Q9BU76
GTEx:  ENSG00000143793 
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Entity ID: 1
MoleculeChains LengthOrganismImage
MSE-U12_exonA [auth 0]57Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
MSE-U12_IntronB [auth 1]277Homo sapiens
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
U12 snRNAC [auth 2]150Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
U5 snRNAE [auth 5]117Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 6
MoleculeChains LengthOrganismImage
U6atac snRNAF [auth 6]125Homo sapiens
Sequence Annotations
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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
NB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
(Subject of Investigation/LOI)

Query on GTP


Download:Ideal Coordinates CCD File
OB [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
WB [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
QB [auth C],
RB [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
TB [auth S],
UB [auth Y]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
(Subject of Investigation/LOI)

Query on K


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

Query on MG


Download:Ideal Coordinates CCD File
FB [auth 6]
GB [auth 6]
HB [auth 6]
IB [auth 6]
LB [auth 6]
FB [auth 6],
GB [auth 6],
HB [auth 6],
IB [auth 6],
LB [auth 6],
MB [auth 6],
PB [auth B],
SB [auth C],
VB [auth v]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		P [auth J]L-PEPTIDE LINKINGC3 H8 N O6 PSER
UNK
Query on UNK		DA [auth X1]L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
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