8I0R

The cryo-EM structure of human Bact-I complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the activation of human spliceosome.

Zhan, X.Lu, Y.Shi, Y.

(2024) Nat Commun 15: 6348-6348

  • DOI: https://doi.org/10.1038/s41467-024-50785-0
  • Primary Citation of Related Structures:  
    8I0P, 8I0R, 8I0S, 8I0T, 8I0U, 8I0V, 8I0W

  • PubMed Abstract: 

    The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (B act complex) and the catalytically activated spliceosome (B * complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B * complexes: pre-B act , B act -I, B act -II, B act -III, B act -IV, and post-B act . Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5'-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation.


  • Organizational Affiliation

    Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. zhanxiechao@westlake.edu.cn.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa protein357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RING finger protein 113A343Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000125352 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like protein802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologM [auth N]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22N [auth O]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologO [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicase aquariusP [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1Q [auth R]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16R [auth S]1,041Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000204560 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1S [auth T]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2T [auth U]2,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologU [auth V]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown polymerV [auth W]122Homo sapiensMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1W [auth X]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163877 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2X [auth Y]322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134597 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
BUD13 homologY [auth Z]619Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137656 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1Z [auth 1]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3AA [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''BA [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3CA [auth w]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1DA [auth u]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2EA [auth 2]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4FA [auth 4]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6GA [auth 6]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115128 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AHA [auth 7]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5IA [auth 5]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RING-type E3 ubiquitin-protein ligase PPIL2JA [auth 9]520Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000100023 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1KA [auth 8]904Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133226 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase ELA [auth y]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: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2MA [auth v]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'NA [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2OA [auth h],
YA [auth c]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FPA [auth i],
ZA [auth d]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'QA [auth m],
WA [auth a]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3CB [auth g],
RA [auth l]
126Homo sapiensMutation(s): 0 
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Find proteins for P62318 (Homo sapiens)
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PHAROS:  P62318
GTEx:  ENSG00000100028 
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UniProt GroupP62318
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GBB [auth f],
SA [auth k]
76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens)
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PHAROS:  P62308
GTEx:  ENSG00000143977 
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UniProt GroupP62308
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EAB [auth e],
TA [auth j]
92Homo sapiensMutation(s): 0 
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Find proteins for P62304 (Homo sapiens)
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PHAROS:  P62304
GTEx:  ENSG00000182004 
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UniProt GroupP62304
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1UA [auth n],
XA [auth b]
119Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens)
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PHAROS:  P62314
GTEx:  ENSG00000167088 
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UniProt GroupP62314
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologVA [auth z]472Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UX04 (Homo sapiens)
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PHAROS:  Q6UX04
GTEx:  ENSG00000153015 
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UniProt GroupQ6UX04
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA117Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
U6 snRNA107Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
pre-mRNA220unidentified adenovirus
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Entity ID: 8
MoleculeChains LengthOrganismImage
U2 snRNA188Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
DB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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EB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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LB [auth K]
MB [auth N]
NB [auth N]
OB [auth N]
PB [auth 7]
LB [auth K],
MB [auth N],
NB [auth N],
OB [auth N],
PB [auth 7],
QB [auth 7],
RB [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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FB [auth C]
GB [auth F]
HB [auth F]
IB [auth F]
JB [auth F]
FB [auth C],
GB [auth F],
HB [auth F],
IB [auth F],
JB [auth F],
KB [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
Z [auth 1]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 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary