9UPB | pdb_00009upb

Structure of the human TREX-2 bound to UAP56

• PDB DOI: https://doi.org/10.2210/pdb9UPB/pdb
• EM Map EMD-64390: EMDB EMDataResource

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


• Deposited: 2025-04-28 Released: 2026-02-18 
• Deposition Author(s): Zhang, X., Gong, X., Ge, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the human TREX-2 bound to UAP56

Zhang, X., Gong, X., Ge, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 161.99 kDa 
• Atom Count: 8,266 
• Modeled Residue Count: 1,021 
• Deposited Residue Count: 1,414 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Germinal-center associated nuclear protein	A	463	Homo sapiens	Mutation(s): 0  Gene Names: MCM3AP, GANP, KIAA0572, MAP80 EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60318 (Homo sapiens) Explore O60318  Go to UniProtKB:  O60318
PHAROS:  O60318 GTEx:  ENSG00000160294

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein 2	B	426	Homo sapiens	Mutation(s): 0  Gene Names: PCID2, HT004
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JVF3 (Homo sapiens) Explore Q5JVF3  Go to UniProtKB:  Q5JVF3
PHAROS:  Q5JVF3 GTEx:  ENSG00000126226

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	C	70	Homo sapiens	Mutation(s): 0  Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
UniProt & NIH Common Fund Data Resources
Find proteins for P60896 (Homo sapiens) Explore P60896  Go to UniProtKB:  P60896
PHAROS:  P60896 GTEx:  ENSG00000127922

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spliceosome RNA helicase DDX39B	D	455	Homo sapiens	Mutation(s): 0  Gene Names: DDX39B, BAT1, UAP56 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q13838 (Homo sapiens) Explore Q13838  Go to UniProtKB:  Q13838
PHAROS:  Q13838 GTEx:  ENSG00000198563

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	E [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Zhang, X., Gong, X., Ge, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32471302

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release