8XWQ

Cryo-EM structure of ET-1 bound ETBR-DNGI complex

PDB DOI: https://doi.org/10.2210/pdb8XWQ/pdb
EM Map EMD-38741: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-01-16 Released: 2024-10-02
Deposition Author(s): Tani, K., Maki-Yonekura, S., Kanno, R., Negami, T., Hamaguchi, T., Hall, M., Mizoguchi, A., Humbel, B.M., Terada, T., Yonekura, K., Doi, T.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.60 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

Structure of endothelin ETB receptor-Gi complex in a conformation stabilized by the unique NPxxL motif

Tani, K., Maki-Yonekura, S., Kanno, R., Negami, T., Hamaguchi, T., Hall, M., Mizoguchi, A., Humbel, B.M., Terada, T., Yonekura, K., Doi, T.

(2024) Commun Biol

DOI: https://doi.org/10.1038/s42003-024-06905-z

Macromolecule Content

Total Structure Weight: 156.65 kDa
Atom Count: 9,076
Modelled Residue Count: 1,163
Deposited Residue Count: 1,413
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelin receptor type B	A [auth R]	346	Homo sapiens	Mutation(s): 0 Gene Names: EDNRB, ETRB
UniProt & NIH Common Fund Data Resources
Find proteins for P24530 (Homo sapiens) Explore P24530 Go to UniProtKB: P24530
PHAROS: P24530 GTEx: ENSG00000136160
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24530
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelin-1	B [auth L]	21	Homo sapiens	Mutation(s): 0 Gene Names: EDN1
UniProt & NIH Common Fund Data Resources
Find proteins for P05305 (Homo sapiens) Explore P05305 Go to UniProtKB: P05305
PHAROS: P05305 GTEx: ENSG00000078401
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05305
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth A]	354	Homo sapiens	Mutation(s): 0 Gene Names: GNAI1
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	344	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth C]	71	Homo sapiens	Mutation(s): 0 Gene Names: GNG2
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
SCFV16	F [auth D]	277	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101118
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121004
Japan Society for the Promotion of Science (JSPS)	Japan	20H03210