7EVN | pdb_00007evn

The cryo-EM structure of the DDX42-SF3b complex

• PDB DOI: https://doi.org/10.2210/pdb7EVN/pdb
• EM Map EMD-31330: EMDB EMDataResource

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


• Deposited: 2021-05-21 Released: 2022-08-03 
• Deposition Author(s): Zhang, X., Zhan, X., Shi, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into branch site proofreading by human spliceosome

Zhang, X., Zhan, X., Bian, T., Yang, F., Li, P., Lu, Y., Xing, Z., Fan, R., Zhang, Q.C., Shi, Y.

(2024) Nat Struct Mol Biol 

• DOI: https://doi.org/10.1038/s41594-023-01188-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 365.73 kDa 
• Atom Count: 19,668 
• Modeled Residue Count: 2,649 
• Deposited Residue Count: 3,276 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 5	A [auth B]	86	Homo sapiens	Mutation(s): 0  Gene Names: SF3B5, SF3B10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWJ5 (Homo sapiens) Explore Q9BWJ5  Go to UniProtKB:  Q9BWJ5
PHAROS:  Q9BWJ5 GTEx:  ENSG00000169976

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 1	B [auth C]	872	Homo sapiens	Mutation(s): 0  Gene Names: SF3B1, SAP155
UniProt & NIH Common Fund Data Resources
Find proteins for O75533 (Homo sapiens) Explore O75533  Go to UniProtKB:  O75533
PHAROS:  O75533 GTEx:  ENSG00000115524

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger-like domain-containing protein 5A	C [auth D]	110	Homo sapiens	Mutation(s): 0  Gene Names: PHF5A
UniProt & NIH Common Fund Data Resources
Find proteins for Q7RTV0 (Homo sapiens) Explore Q7RTV0  Go to UniProtKB:  Q7RTV0
PHAROS:  Q7RTV0 GTEx:  ENSG00000100410

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 3	D [auth A]	1,250	Homo sapiens	Mutation(s): 0  Gene Names: SF3B3, KIAA0017, SAP130
UniProt & NIH Common Fund Data Resources
Find proteins for Q15393 (Homo sapiens) Explore Q15393  Go to UniProtKB:  Q15393
PHAROS:  Q15393 GTEx:  ENSG00000189091

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX42	E	958	Homo sapiens	Mutation(s): 0  Gene Names: DDX42 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q86XP3 (Homo sapiens) Explore Q86XP3  Go to UniProtKB:  Q86XP3
PHAROS:  Q86XP3 GTEx:  ENSG00000198231

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	F [auth D], G [auth D], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Zhang, X., Zhan, X., Shi, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31930059

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Database references
• Version 1.3: 2025-06-18
  Changes: Data collection, Structure summary