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 8POK | pdb_00008pok

Cryo-EM structure of cell-free synthesized human histamine H2 receptor coupled to heterotrimeric Gs protein in lipid environment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8POK

This is version 1.3 of the entry. See complete history. 

Literature

Cryo-EM structure of cell-free synthesized human histamine 2 receptor/G s complex in nanodisc environment.

Kock, Z., Schnelle, K., Persechino, M., Umbach, S., Schihada, H., Januliene, D., Parey, K., Pockes, S., Kolb, P., Dotsch, V., Moller, A., Hilger, D., Bernhard, F.

(2024) Nat Commun 15: 1831-1831

  • DOI: https://doi.org/10.1038/s41467-024-46096-z
  • Primary Citation Related Structures: 
    8POK

  • PubMed Abstract: 

    Here we describe the cryo-electron microscopy structure of the human histamine 2 receptor (H 2 R) in an active conformation with bound histamine and in complex with G s heterotrimeric protein at an overall resolution of 3.4 Å. The complex was generated by cotranslational insertion of the receptor into preformed nanodisc membranes using cell-free synthesis in E. coli lysates. Structural comparison with the inactive conformation of H 2 R and the inactive and G q -coupled active state of H 1 R together with structure-guided functional experiments reveal molecular insights into the specificity of ligand binding and G protein coupling for this receptor family. We demonstrate lipid-modulated folding of cell-free synthesized H 2 R, its agonist-dependent internalization and its interaction with endogenously synthesized H 1 R and H 2 R in HEK293 cells by applying a recently developed nanotransfer technique.


  • Organizational Affiliation: 
    • Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt, Germany.

Macromolecule Content 

  • Total Structure Weight: 146.87 kDa 
  • Atom Count: 8,042 
  • Modeled Residue Count: 1,024 
  • Deposited Residue Count: 1,306 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histamine H2 receptor375Homo sapiensMutation(s): 0 
Gene Names: HRH2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25021 (Homo sapiens)
Explore P25021 
Go to UniProtKB:  P25021
PHAROS:  P25021
GTEx:  ENSG00000113749 
Entity Groups
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UniProt GroupP25021
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short380Homo sapiensMutation(s): 0 
Gene Names: GNAS, GNAS1, GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-268Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody35138Lama glamaMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HSM
(Subject of Investigation/LOI)

Query on HSM



Download:Ideal Coordinates CCD File
F [auth A]HISTAMINE
C5 H9 N3
NTYJJOPFIAHURM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGLUE
Other privateSK-208/16
German Research Foundation (DFG)Germany944 (P27)
German Research Foundation (DFG)Germany1557 (P11)
German Research Foundation (DFG)GermanyINST 190-196-1 FUGG
Other governmentGermanySPRUNG Stay inspired 15-76251-2-04/22 (10743/2022)

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection