6CIL

PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+

• PDB DOI:  https://doi.org/10.2210/pdb6CIL/pdb
• NAKB: 6CIL

• Classification: RECOMBINATION/DNA
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-02-24 Released: 2018-04-25 
• Deposition Author(s): Chuenchor, W., Chen, X., Kim, M.S., Gellert, M., Yang, W.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.15 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Cracking the DNA Code for V(D)J Recombination.

Kim, M.S., Chuenchor, W., Chen, X., Cui, Y., Zhang, X., Zhou, Z.H., Gellert, M., Yang, W.

(2018) Mol Cell 70: 358-370.e4

• PubMed: 29628308 
• DOI: https://doi.org/10.1016/j.molcel.2018.03.008
• Primary Citation of Related Structures:  
  5ZDZ, 5ZE0, 5ZE1, 5ZE2, 6CG0, 6CIJ, 6CIK, 6CIL, 6CIM


• PubMed Abstract: 
  

To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.

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Organizational Affiliation: 

Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 301.16 kDa 
• Atom Count: 18,260 
• Modelled Residue Count: 2,076 
• Deposited Residue Count: 2,321 
• Unique protein chains: 3
• 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	625	Mus musculus	Mutation(s): 1  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	359	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	Sequence Length	Organism	Details	Image
High mobility group protein B1	E [auth N]	163	Homo sapiens	Mutation(s): 0  Gene Names: HMGB1, HMG1
UniProt & NIH Common Fund Data Resources
Find proteins for P09429 (Homo sapiens) Explore P09429  Go to UniProtKB:  P09429
PHAROS:  P09429

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Intact 12RSS substrate reverse strand	F	40	Homo sapiens

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Intact 12RSS substrate forward strand	G [auth I]	40	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Intact 23RSS substrate reverse strand	H [auth G]	55	Homo sapiens

Entity ID: 7
Molecule	Chains	Length	Organism	Image
Intact 23RSS substrate forward strand	I [auth J]	55	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	J [auth A], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	K [auth A], M [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.15 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.332	α = 90
b = 118.83	β = 100.59
c = 198.96	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALA	data scaling
PHENIX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Chuenchor, W., Chen, X., Kim, M.S., Gellert, M., Yang, W.

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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	DK036147, DK036144, DK036167
National Institutes of Health/Office of the Director	United States	--

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2022-03-23
  Changes: Author supporting evidence, Database references