3JBX | pdb_00003jbx

Cryo-electron microscopy structure of RAG Signal End Complex (C2 symmetry)

• PDB DOI: https://doi.org/10.2210/pdb3JBX/pdb
• NAKB: 3JBX
• EM Map EMD-6487: EMDB EMDataResource

• Classification: RECOMBINATION/DNA
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-10-22 Released: 2015-12-09 
• Deposition Author(s): Ru, H., Chambers, M.G., Fu, T.-M., Tong, A.B., Liao, M., Wu, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.

Ru, H., Chambers, M.G., Fu, T.M., Tong, A.B., Liao, M., Wu, H.

(2015) Cell 163: 1138-1152

• PubMed: 26548953 
• DOI: https://doi.org/10.1016/j.cell.2015.10.055
• Primary Citation Related Structures: 
  3JBW, 3JBX, 3JBY


• PubMed Abstract: 
  

  Diverse repertoires of antigen-receptor genes that result from combinatorial splicing of coding segments by V(D)J recombination are hallmarks of vertebrate immunity. The (RAG1-RAG2)2 recombinase (RAG) recognizes recombination signal sequences (RSSs) containing a heptamer, a spacer of 12 or 23 base pairs, and a nonamer (12-RSS or 23-RSS) and introduces precise breaks at RSS-coding segment junctions. RAG forms synaptic complexes only with one 12-RSS and one 23-RSS, a dogma known as the 12/23 rule that governs the recombination fidelity. We report cryo-electron microscopy structures of synaptic RAG complexes at up to 3.4 Å resolution, which reveal a closed conformation with base flipping and base-specific recognition of RSSs. Distortion at RSS-coding segment junctions and base flipping in coding segments uncover the two-metal-ion catalytic mechanism. Induced asymmetry involving tilting of the nonamer-binding domain dimer of RAG1 upon binding of HMGB1-bent 12-RSS or 23-RSS underlies the molecular mechanism for the 12/23 rule.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 329.95 kDa 
• Atom Count: 16,670 
• Modeled Residue Count: 1,918 
• Deposited Residue Count: 2,710 
• 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	764	Danio rerio	Mutation(s): 0  Gene Names: rag1 EC: 3.1 (PDB Primary Data), 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for O13033 (Danio rerio) Explore O13033  Go to UniProtKB:  O13033

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V(D)J recombination-activating protein 2	B, D	533	Danio rerio	Mutation(s): 0  Gene Names: rag2, rag-2
UniProt
Find proteins for O13034 (Danio rerio) Explore O13034  Go to UniProtKB:  O13034

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*CP*AP*GP*TP*GP*CP*TP*AP*CP*AP*GP*AP*C)-3'	E, H	15	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*TP*CP*TP*GP*TP*AP*GP*CP*AP*CP*TP*GP*TP*G)-3'	F, G	15	Homo sapiens

Entity ID: 5
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*TP*GP*GP*TP*TP*AP*AP*CP*CP*A)-3'	I, K	14	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*GP*GP*TP*TP*AP*AP*CP*CP*AP*TP*CP*GP*C)-3'	J, L	14	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth A], P [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	N [auth A], O [auth A], Q [auth C], R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Ru, H., Chambers, M.G., Fu, T.-M., Tong, A.B., Liao, M., Wu, H.

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations