6LFM Membrane Protein date Dec 03, 2019
title Cryo-Em Structure Of A Class A Gpcr
authors Z.J.Liu, T.Hua, K.W.Liu, L.J.Wu
compound source
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_taxid: 7108

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gnb1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gng2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Interleukin-8
Chain: D, E
Synonym: Il-8,C-X-C Motif Chemokine 8,Chemokine (C-X-C Moti 8,Emoctakin,Granulocyte Chemotactic Protein 1,Gcp-1,Monocyt Neutrophil Chemotactic Factor,Mdncf,Monocyte-Derived Neutro Activating Peptide,Monap,Neutrophil-Activating Protein 1,Na Protein 3-10c,T-Cell Chemotactic Factor;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cxcl8, Il8
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: C-X-C Chemokine Receptor Type 2
Chain: R
Synonym: Cxcr-2,Cdw128b,Gromgsa Receptor,High Affinity Int Receptor B,Il-8r B,Il-8 Receptor Type 2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cxcr2, Il8rb
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Scfv16
Chain: S
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
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 3.50 Å
ligand CLR enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B
  • G-protein coupled acetylchol...

  • C


    D, E


    R
  • chemokine receptor activity
  • C-C chemokine receptor activ...
  • C-X-C chemokine receptor act...


  • Primary referenceStructural basis of CXC chemokine receptor 2 activation and signalling., Liu K, Wu L, Yuan S, Wu M, Xu Y, Sun Q, Li S, Zhao S, Hua T, Liu ZJ, Nature. 2020 Jul 1. pii: 10.1038/s41586-020-2492-5. doi:, 10.1038/s41586-020-2492-5. PMID:32610344
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (204 Kb) [Save to disk]
  • Biological Unit Coordinates (6lfm.pdb1.gz) 195 Kb
  • LPC: Ligand-Protein Contacts for 6LFM
  • CSU: Contacts of Structural Units for 6LFM
  • Retrieve 6LFM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6LFM from S2C, [Save to disk]
  • View 6LFM 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 6LFM
  • 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 6lfm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6lfm_R] [6lfm_A] [6lfm_B] [6lfm_D] [6lfm_S] [6lfm_C] [6lfm_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6LFM
  • Community annotation for 6LFM at PDBWiki (http://pdbwiki.org)

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