9DLP | pdb_00009dlp

Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56)

• PDB DOI: https://doi.org/10.2210/pdb9DLP/pdb
• EM Map EMD-46982: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-11 Released: 2025-06-04 
• Deposition Author(s): Clarke, B.P., Xie, Y., Ren, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms of mRNP remodeling by human TREX-2 complex

Clarke, B.P., Xie, Y., Ren, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 177.01 kDa 
• Atom Count: 8,522 
• Modeled Residue Count: 1,049 
• Deposited Residue Count: 1,550 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Germinal-center associated nuclear protein	A	648	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	399	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	433	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	E [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Clarke, B.P., Xie, Y., Ren, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release