9BKJ

Cholecystokinin 1 receptor (CCK1R) Y140A mutant, Gq chimera (mGsqi) complex

PDB DOI: https://doi.org/10.2210/pdb9BKJ/pdb
EM Map EMD-44642: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2024-04-29 Released: 2024-05-22
Deposition Author(s): Cary, B.P., Harikumar, K.G., Zhao, P., Desai, A.J., Mobbs, J.M., Toufaily, C., Furness, S.G.B., Christopoulos, A., Belousoff, M.J., Wootten, D., Sexton, P.M., Miller, L.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 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

Cholesterol-dependent dynamic changes in the conformation of the type 1 cholecystokinin receptor affect ligand binding and G protein coupling

Harikumar, K.G., Zhao, P., Cary, B.P., Xu, X., Desai, A.J., Mobbs, J.I., Toufaily, C., Furness, S.G.B., Christopoulos, A., Belousoff, M.J., Wootten, D., Sexton, P.M., Miller, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 121.76 kDa
Atom Count: 6,795
Modelled Residue Count: 891
Deposited Residue Count: 1,086
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth G]	58	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholecystokinin-8	C [auth P]	8	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P06307 (Homo sapiens) Explore P06307 Go to UniProtKB: P06307
PHAROS: P06307 GTEx: ENSG00000187094
Entity Groups
UniProt Group	P06307
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholecystokinin receptor type A	D [auth R]	427	Homo sapiens	Mutation(s): 1 Gene Names: CCKAR, CCKRA Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P32238 (Homo sapiens) Explore P32238 Go to UniProtKB: P32238
PHAROS: P32238 GTEx: ENSG00000163394
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32238
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	E [auth A]	253	Homo sapiens	Mutation(s): 24 Gene Names: GNAI1, GNAS, GNAS1, GSP 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
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092
PHAROS: P63092 GTEx: ENSG00000087460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P63096P63092
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NH2 (Subject of Investigation/LOI) Query on NH2 Download Ideal Coordinates CCD File SDF format, chain F [auth P] MOL2 format, chain F [auth P]	F [auth P]	AMINO GROUP H₂ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain F [auth P] Interactions & Density Focus chain F [auth P]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	C [auth P]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM141003
National Health and Medical Research Council (NHMRC, Australia)	Australia	1154434
National Health and Medical Research Council (NHMRC, Australia)	Australia	1155302
Australian Research Council (ARC)	Australia	FT180100543