7NA7 | pdb_00007na7

Structures of human ghrelin receptor-Gi complexes with ghrelin and a synthetic agonist

PDB DOI: https://doi.org/10.2210/pdb7NA7/pdb
EM Map EMD-24267: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Insect expression vector pBlueBacmsGCA1His
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-06-20 Released: 2021-12-15
Deposition Author(s): Liu, H., Sun, D., Sun, J., Zhang, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of human ghrelin receptor signaling by ghrelin and the synthetic agonist ibutamoren

Liu, H., Sun, D., Myasnikov, A., Damian, M., Baneres, J.L., Sun, J., Zhang, C.

(2021) Nat Commun 12: 6410

DOI: https://doi.org/10.1038/s41467-021-26735-5

Macromolecule Content

Total Structure Weight: 155.59 kDa
Atom Count: 9,036
Modeled Residue Count: 1,142
Deposited Residue Count: 1,389
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 0 Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment	D [auth N]	246	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth hormone secretagogue receptor type 1	E [auth R]	366	Homo sapiens	Mutation(s): 0 Gene Names: GHSR Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q92847 (Homo sapiens) Explore Q92847 Go to UniProtKB: Q92847
PHAROS: Q92847 GTEx: ENSG00000121853
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92847
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ghrelin-27	F [auth L]	12	Homo sapiens	Mutation(s): 1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBU3 (Homo sapiens) Explore Q9UBU3 Go to UniProtKB: Q9UBU3
PHAROS: Q9UBU3 GTEx: ENSG00000157017
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR (Subject of Investigation/LOI) Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth R] SDF format, chain H [auth R] MOL2 format, chain G [auth R] MOL2 format, chain H [auth R] mmCIF format, chain G [auth R] mmCIF format, chain H [auth R]	G [auth R], H [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth R] Focus chain H [auth R] Interactions & Density Focus chain G [auth R] Focus chain H [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128641
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R03TR003306