6XJD Immune System Dna date Jun 23, 2020
title Two Mouse Cgas Catalytic Domain Binding To Human Assembled N
authors P.Xu, P.Li, B.Zhao
compound source
Molecule: Histone H3.2
Chain: A, E
Synonym: H3-Clustered Histone 13,H3-Clustered Histone 14,H3 Histone 15,Histone H3m,Histone H3o;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3c15, Hist2h3a, H3c14, H3f2, H3fm, Hist2h3c, H3c13,
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Histone H2a Type 1
Chain: C, G
Synonym: H2a.1,Histone H2aptl
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2ac11, H2afp, Hist1h2ag, H2ac13, H2afc, Hist1h2ai, H H2afd, Hist1h2ak, H2ac16, H2afi, Hist1h2al, H2ac17, H2afn, Hist1h2am;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Histone H2b Type 1-Cefgi
Chain: D, H
Synonym: Histone H2b.1 A,Histone H2b.A,H2ba,Histone H2b.G, Histone H2b.H,H2bh,Histone H2b.K,H2bk,Histone H2b.L,H2bl
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2bc4, H2bfl, Hist1h2bc, H2bc6, H2bfh, Hist1h2be, H2b H2bfg, Hist1h2bf, H2bc8, H2bfa, Hist1h2bg, H2bc10, H2bfk, H
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Cyclic Gmp-Amp Synthase
Chain: K, L
Synonym: M-Cgas,2'3'-Cgamp Synthase,Mab-21 Domain-Containin 1;
Ec: 2.7.7.86
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Cgas, Mb21d1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
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 6.80 Å
ligand ZN enzyme Transferase E.C.2.7.7.86 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceThe Molecular Basis of Tight Nuclear Tethering and Inactivation of cGAS., Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P, Nature. 2020 Sep 10. pii: 10.1038/s41586-020-2749-z. doi:, 10.1038/s41586-020-2749-z. PMID:32911481
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (324 Kb) [Save to disk]
  • Biological Unit Coordinates (6xjd.pdb1.gz) 312 Kb
  • LPC: Ligand-Protein Contacts for 6XJD
  • CSU: Contacts of Structural Units for 6XJD
  • Retrieve 6XJD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6XJD from S2C, [Save to disk]
  • View 6XJD 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 6XJD
  • 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 6xjd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6xjd_F] [6xjd_D] [6xjd_L] [6xjd_E] [6xjd_B] [6xjd_H] [6xjd_I] [6xjd_A] [6xjd_C] [6xjd_K] [6xjd_G] [6xjd_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6XJD
  • Community annotation for 6XJD at PDBWiki (http://pdbwiki.org)

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