6CIK

Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.molcel.2018.03.008
  • Primary Citation of Related Structures:  

  • 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 wi ...

    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.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA; Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 1
A, C
625Mus musculusMutation(s): 1 
Gene Names: Rag1
Find proteins for P15919 (Mus musculus)
Go to UniProtKB:  P15919
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 2
B, D
359Mus musculusMutation(s): 0 
Gene Names: Rag2 (Rag-2)
Find proteins for P21784 (Mus musculus)
Go to UniProtKB:  P21784
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
High mobility group protein B1
N
163Homo sapiensMutation(s): 0 
Gene Names: HMGB1 (HMG1)
Find proteins for P09429 (Homo sapiens)
Go to Gene View: HMGB1
Go to UniProtKB:  P09429
Entity ID: 4
MoleculeChainsLengthOrganism
Intact 12RSS substrate reverse strandF39Homo sapiens
Entity ID: 5
MoleculeChainsLengthOrganism
Intact 12RSS substrate forward strandI40Homo sapiens
Entity ID: 6
MoleculeChainsLengthOrganism
Nicked 23RSS intermediate reverse strandG55Homo sapiens
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')J15Homo sapiens
Entity ID: 8
MoleculeChainsLengthOrganism
Nicked 23RSS intermediate forward strandM40Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.423α = 90.00
b = 123.149β = 105.03
c = 186.327γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institute of Diabetes and Digestive and Kidney DiseasesUnited StatesDK036147, DK036144, DK036167
National Institutes of Health Intramural AIDS targeted Anti-viral ProgramUnited States--

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references