6Y5D Immune System date Feb 25, 2020
title Structure Of Human Cgas (K394e) Bound To The Nucleosome
authors G.R.Pathare, S.Cavadini, G.Kempf, N.H.Thoma
compound source
Molecule: Histone H3.2
Chain: A, E, M, Q
Synonym: Histone H3m,Histone H3o
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist2h3a, Hist2h3c, H3f2, H3fm, Hist2h3d
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333

Molecule: Histone H4
Chain: B, F, N, R
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 K-12
Expression_system_taxid: 83333

Molecule: Histone H2a Type 2-A
Chain: C, G, O, S
Synonym: Histone H2a.2,Histone H2ao
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist2h2aa3, H2afo, Hist2h2aa, Hist2h2aa4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-K
Chain: D, H, P, T
Synonym: H2b K,Hira-Interacting Protein 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bk, H2bft, Hirip1
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333

Molecule: Dna (153-Mer)
Chain: I, U
Engineered: Yes

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

Molecule: Dna (153-Mer)
Chain: J, V
Engineered: Yes

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

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cgas, C6orf150, Mb21d1
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333
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 4.10 Å
ligand PTD, ZN enzyme Transferase E.C.2.7.7.86 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, N, B, R


S, O, C, G


T, P, H, D


Primary referenceStructural mechanism of cGAS inhibition by the nucleosome., Pathare GR, Decout A, Gluck S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thoma NH, Ablasser A, Nature. 2020 Sep 10. pii: 10.1038/s41586-020-2750-6. doi:, 10.1038/s41586-020-2750-6. PMID:32911482
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (593 Kb) [Save to disk]
  • Biological Unit Coordinates (6y5d.pdb1.gz) 577 Kb
  • LPC: Ligand-Protein Contacts for 6Y5D
  • CSU: Contacts of Structural Units for 6Y5D
  • Retrieve 6Y5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6Y5D from S2C, [Save to disk]
  • View 6Y5D 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 6Y5D
  • 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 6y5d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6y5d_H] [6y5d_M] [6y5d_N] [6y5d_B] [6y5d_J] [6y5d_D] [6y5d_P] [6y5d_U] [6y5d_K] [6y5d_I] [6y5d_T] [6y5d_E] [6y5d_C] [6y5d_R] [6y5d_S] [6y5d_A] [6y5d_Q] [6y5d_V] [6y5d_F] [6y5d_L] [6y5d_O] [6y5d_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6Y5D
  • Community annotation for 6Y5D at PDBWiki (http://pdbwiki.org)

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