5ZDZ

Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 

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
mouse RAG1
A, C
627Mus musculusMutation(s): 0 
Gene Names: Rag1
Find proteins for P15919 (Mus musculus)
Go to UniProtKB:  P15919
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
mouse RAG2
B, D
389Mus musculusMutation(s): 1 
Gene Names: Rag2 (Rag-2)
Find proteins for P21784 (Mus musculus)
Go to UniProtKB:  P21784
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HMGB1 A-B box
N
163Mus musculusMutation(s): 0 
Gene Names: Hmgb1 (Hmg-1, Hmg1)
Find proteins for P63158 (Mus musculus)
Go to UniProtKB:  P63158
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')F45synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (54-MER)I16synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (30-MER)J16synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (39-MER)G54synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
DNA chain LL30synthetic construct
Entity ID: 9
MoleculeChainsLengthOrganism
DNA chain MM39synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 132.450α = 90.00
b = 109.000β = 114.28
c = 156.050γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIHUnited States--

Revision History 

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