[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleCracking the DNA Code for V(D)J Recombination.
Journal, issue, pagesMol Cell, Vol. 70, Issue 2, Page 358-370.e4, Year 2018
Publish dateApr 19, 2018
AuthorsMin-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang /
PubMed AbstractTo 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 ...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.
External linksMol Cell / PubMed:29628308 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.75 - 4.15 Å
Structure data

7470

6cg0

EMDB-7470: RAG1/2 HFC complex
PDB-6cg0: Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A)
Method: EM (single particle) / Resolution: 3.17 Å

7480

6cij

EMDB-7480, PDB-6cij:
Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
Method: EM (single particle) / Resolution: 3.9 Å

PDB-5zdz:
Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-5ze0:
Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-5ze1:
Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-5ze2:
Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-6cik:
Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+
Method: X-RAY DIFFRACTION / Resolution: 3.15 Å

PDB-6cil:
PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+
Method: X-RAY DIFFRACTION / Resolution: 4.15 Å

PDB-6cim:
Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-MN:
Unknown entry

Source
  • mus musculus (house mouse)
  • homo sapiens (human)
  • escherichia coli k-12 (bacteria)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / V(D)J recombination / RAG1-2-12RSS-23RSS complex / Hairpin forming complex / Hairpin complex / RECOMBINATION / RAG1/2 / RSS / Immunity / RECOMBINATION/DNA / RECOMBINATION-DNA complex / VDJ recombination

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more