9JPU | pdb_00009jpu

CryoEM structure of mouse RAG SEC-PHD

• PDB DOI: https://doi.org/10.2210/pdb9JPU/pdb
• NAKB: 9JPU
• EM Map EMD-61715: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mus musculus, Escherichia coli
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-26 Released: 2025-07-23 
• Deposition Author(s): Chen, X., Yao, L., Yang, W., Gellert, M.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of mouse RAG SEC-PHD

Chen, X., Yao, L., Yang, W., Gellert, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 434.27 kDa 
• Atom Count: 15,963 
• Modeled Residue Count: 1,911 
• Deposited Residue Count: 3,719 
• Unique protein chains: 2
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V(D)J recombination-activating protein 1	A, C	1,040	Mus musculus	Mutation(s): 0  Gene Names: Rag1 EC: 3.1 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
UniProt
Find proteins for P15919 (Mus musculus) Explore P15919  Go to UniProtKB:  P15919

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V(D)J recombination-activating protein 2	B, D, I [auth E]	527	Mus musculus	Mutation(s): 0  Gene Names: Rag2, Rag-2
UniProt
Find proteins for P21784 (Mus musculus) Explore P21784  Go to UniProtKB:  P21784

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3')	E [auth F]	15	Escherichia coli

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3')	F [auth G]	14	Escherichia coli

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')	G [auth L]	15	Escherichia coli

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')	H [auth M]	14	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	K [auth A], M [auth C], N [auth E], O [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	J [auth A], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 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: 2025-07-23 
Deposition Author(s): Chen, X., Yao, L., Yang, W., Gellert, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release