6DBO Recombination Dna date May 03, 2018
title Cryo-Em Structure Of Rag In Complex With 12-Rss And 23-Rss S Dnas
authors H.Wu, M.Liao, H.Ru, W.Mi
compound source
Molecule: Recombination Activating Gene 1 - Mbp Chimera
Chain: A, C
Synonym: Rag-1
Ec: 2.3.2.27
Engineered: Yes
Organism_scientific: Escherichia Coli, Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 83333, 7955
Strain: K12
Gene: Male, B4034, Jw3994, Rag1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Recombination Activating Gene 2
Chain: B, D
Synonym: V(D)J Recombination-Activating Protein 2
Engineered: Yes

Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Gene: Rag2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Forward Strand Of Substrate Rss Dna
Chain: E, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Danio Rerio
Organism_taxid: 7955

Molecule: Reverse Strand Of Substrate Rss Dna
Chain: F, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Danio Rerio
Organism_taxid: 7955
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.45 Å
ligand CA, ZN enzyme Transferase E.C.2.3.2.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • carbohydrate transmembrane t...


  • D, B


    Primary referenceDNA melting initiates the RAG catalytic pathway., Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H, Nat Struct Mol Biol. 2018 Aug;25(8):732-742. doi: 10.1038/s41594-018-0098-5. Epub, 2018 Jul 30. PMID:30061602
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (360 Kb) [Save to disk]
  • Biological Unit Coordinates (6dbo.pdb1.gz) 347 Kb
  • LPC: Ligand-Protein Contacts for 6DBO
  • CSU: Contacts of Structural Units for 6DBO
  • Retrieve 6DBO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DBO from S2C, [Save to disk]
  • View 6DBO in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6DBO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6dbo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6dbo_D] [6dbo_G] [6dbo_H] [6dbo_F] [6dbo_A] [6dbo_B] [6dbo_E] [6dbo_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6DBO
  • Community annotation for 6DBO at PDBWiki (http://pdbwiki.org)

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