5ZE1

Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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.


  • 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mouse RAG1
A, C
627Mus musculusMutation(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
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UniProt GroupP15919
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mouse RAG2
B, D
389Mus musculusMutation(s): 1 
Gene Names: Rag2Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
Explore P21784 
Go to UniProtKB:  P21784
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UniProt GroupP21784
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HMGB1 A-B boxE [auth N]163Mus musculusMutation(s): 0 
Gene Names: Hmgb1Hmg-1Hmg1
UniProt
Find proteins for P63158 (Mus musculus)
Explore P63158 
Go to UniProtKB:  P63158
Entity Groups  
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UniProt GroupP63158
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA45synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNAG [auth I]16synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNAH [auth J]16synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNAI [auth G]54synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNAJ [auth L]30synthetic construct
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNAK [auth M]39synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
L [auth A],
Q [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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O [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

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M [auth A],
N [auth A],
R [auth C],
S [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
P [auth A],
T [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.76α = 90
b = 108.6β = 114.2
c = 157.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIHUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations