6CMO Signaling Protein date Mar 05, 2018
title Rhodopsin-Gi Complex
authors Y.Kang, O.Kuybeda, P.W.De Waal, S.Mukherjee, N.Van Eps, P.Dutka, X A.Bartesaghi, S.Erramilli, T.Morizumi, X.Gu, Y.Yin, P.Liu, Y.Jian G.Zhao, K.Melcher, O.P.Earnst, A.A.Kossiakoff, S.Subramaniam, H.
compound source
Molecule: Chimera Protein Of Soluble Cytochrome B562 And Rh
Chain: R
Synonym: Cytochrome B-562,Opsin-2
Engineered: Yes
Organism_scientific: Escherichia Coli, Homo Sapiens
Organism_common: Human
Organism_taxid: 562, 9606
Gene: Cybc, Rho, Opn2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Guanine Nucleotide-Binding Protein G(I) Subunit A
Chain: A
Synonym: Adenylate Cyclase-Inhibiting G Alpha Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gnai1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Guanine Nucleotide-Binding Protein G(I)G(S)G(T) Beta-1;
Chain: B
Synonym: Transducin Beta Chain 1
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Gnb1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Guanine Nucleotide-Binding Protein G(I)G(S)G(O) Gamma-2;
Chain: G
Synonym: G Gamma-I
Engineered: Yes

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Gene: Gng2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Fab Light Chain
Chain: L
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Bacteria Latreille Et Al. 1825
Expression_system_taxid: 629395

Molecule: Fab Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Bacteria Latreille Et Al. 1825
Expression_system_taxid: 629395
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 4.50 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


G


R


Primary referenceCryo-EM structure of human rhodopsin bound to an inhibitory G protein., Kang Y, Kuybeda O, de Waal PW, Mukherjee S, Van Eps N, Dutka P, Zhou XE, Bartesaghi A, Erramilli S, Morizumi T, Gu X, Yin Y, Liu P, Jiang Y, Meng X, Zhao G, Melcher K, Ernst OP, Kossiakoff AA, Subramaniam S, Xu HE, Nature. 2018 Jun;558(7711):553-558. doi: 10.1038/s41586-018-0215-y. Epub 2018 Jun, 13. PMID:29899450
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk]
  • Biological Unit Coordinates (6cmo.pdb1.gz) 223 Kb
  • CSU: Contacts of Structural Units for 6CMO
  • Retrieve 6CMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CMO from S2C, [Save to disk]
  • View 6CMO 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 6CMO
  • 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 6cmo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6cmo_A] [6cmo_L] [6cmo_B] [6cmo_H] [6cmo_R] [6cmo_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CMO
  • Community annotation for 6CMO at PDBWiki (http://pdbwiki.org)

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