9UPB | pdb_00009upb

Structure of the human TREX-2 bound to UAP56

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 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

Structure of the human TREX-2 bound to UAP56

Zhang, X., Gong, X., Ge, X.

To be published.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Germinal-center associated nuclear protein463Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60318
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PCI domain-containing protein 2426Homo sapiensMutation(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 Groups
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UniProt GroupQ5JVF3
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM170Homo sapiensMutation(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 Groups
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UniProt GroupP60896
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome RNA helicase DDX39B455Homo sapiensMutation(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 
Entity Groups
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UniProt GroupQ13838
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
(Subject of Investigation/LOI)

Query on ANP


Download:Ideal Coordinates CCD File
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:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32471302

Revision History  (Full details and data files)

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