6XOX Membrane Protein date Jul 07, 2020
title Cryo-Em Of Human Glp-1r Bound To Non-Peptide Agonist Ly35029
authors B.Sun, B.K.Kobilka, K.W.Sloop, D.Feng, T.S.Kobilka
compound source
Molecule: Alpha Subunit Of Gs With N-Terminus Swapped With Residues In Gi,Guanine Nucleotide-Binding Protein G(S) Subu Isoforms Xlas;
Chain: A
Synonym: Adenylate Cyclase-Stimulating G Alpha Protein,Extr Alphas Protein,Xlalphas;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gnas, Gnas, Gnas1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
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: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gnb1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Single-Chain Variable Fragment Scfv16
Chain: E
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Spodoptera Frugiperda
Expression_system_common: Cabbage Looper
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: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gng2
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Nanobody 35
Chain: N
Engineered: Yes

Organism_scientific: Lama Glama
Organism_taxid: 9844
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Glucagon-Like Peptide 1 Receptor
Chain: R
Synonym: Glp-1r
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Glp1r
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
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 3.10 Å
ligand V6G enzyme
Primary referenceStructural basis for GLP-1 receptor activation by LY3502970, an orally active nonpeptide agonist., Kawai T, Sun B, Yoshino H, Feng D, Suzuki Y, Fukazawa M, Nagao S, Wainscott DB, Showalter AD, Droz BA, Kobilka TS, Coghlan MP, Willard FS, Kawabe Y, Kobilka BK, Sloop KW, Proc Natl Acad Sci U S A. 2020 Nov 11. pii: 2014879117. doi:, 10.1073/pnas.2014879117. PMID:33177239
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (200 Kb) [Save to disk]
  • Biological Unit Coordinates (6xox.pdb1.gz) 191 Kb
  • LPC: Ligand-Protein Contacts for 6XOX
  • CSU: Contacts of Structural Units for 6XOX
  • Retrieve 6XOX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6XOX from S2C, [Save to disk]
  • View 6XOX 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 6XOX
  • 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 6xox from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6xox_R] [6xox_E] [6xox_G] [6xox_A] [6xox_N] [6xox_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6XOX
  • Community annotation for 6XOX at PDBWiki (http://pdbwiki.org)

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