5TDH

The crystal structure of the dominant negative mutant G protein alpha(i)-1-beta-1-gamma-2 G203A/A326S

PDB DOI: https://doi.org/10.2210/pdb5TDH/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-09-19 Released: 2016-11-09
Deposition Author(s): Liu, P., Jia, M.-Z., Zhou, X.E., de Waal, P.W., Dickson, B.M., Liu, B., Hou, L., Yin, Y.-T., Kang, Y.-Y., Shi, Y., Melcher, K., Xu, H.E., Jiang, Y.
Funding Organization(s): National Natural Science Foundation of China, the Shanghai Science and Technology Committee, the Shanghai Rising-Star Program, the Outstanding Young Scientist Foundation, Chinese Academy of Sciences, the Youth Innovation Promotion Association CAS, the SANOFISIBS Scholarship, Amway (China), the Jay and Betty Van Andel Foundation, the Ministry of Science and Technology of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.305
R-Value Work: 0.276
R-Value Observed: 0.278

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This is version 1.2 of the entry. See complete history.

Literature

The structural basis of the dominant negative phenotype of the G alpha i1 beta 1 gamma 2 G203A/A326S heterotrimer

Liu, P., Jia, M.-Z., Zhou, X.E., De Waal, P.W., Dickson, B.M., Liu, B., Hou, L., Yin, Y.-T., Kang, Y.-Y., Shi, Y., Melcher, K., Xu, H.E., Jiang, Y.

(2016) Acta Pharmacol Sin 37: 1259-1272

PubMed: 27498775 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/aps.2016.69
Primary Citation of Related Structures:
5TDH

PubMed Abstract:
Dominant negative mutant G proteins have provided critical insight into the mechanisms of G protein-coupled receptor (GPCR) signaling, but the mechanisms underlying the dominant negative characteristics are not completely understood. The aim of this study was to determine the structure of the dominant negative Gαi1β1γ2 G203A/A326S complex (Gi-DN) and to reveal the structural basis of the mutation-induced phenotype of Gαi1β1γ2.

Organizational Affiliation

VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecule Content

Total Structure Weight: 172.02 kDa
Atom Count: 11,505
Modelled Residue Count: 1,461
Deposited Residue Count: 1,528
Unique protein chains: 3

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) subunit alpha-1	A, D [auth H]	354	Homo sapiens	Mutation(s): 2 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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(by identity cutoff) | 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, E [auth J]	342	Rattus norvegicus	Mutation(s): 0 Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311 Go to UniProtKB: P54311
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54311
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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], F [auth K]	68	Bos taurus	Mutation(s): 0 Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212 Go to UniProtKB: P63212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H MOL2 format, chain G [auth A] MOL2 format, chain H	G [auth A], H	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain H Interactions & Density Focus chain G [auth A] Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.305
R-Value Work: 0.276
R-Value Observed: 0.278
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.009	α = 90
b = 54.57	β = 113.1
c = 138.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31300607
the Shanghai Science and Technology Committee	China	13ZR1447600
the Shanghai Rising-Star Program	China	14QA1404300
the Outstanding Young Scientist Foundation, Chinese Academy of Sciences	China	--
the Youth Innovation Promotion Association CAS	China	--
the SANOFISIBS Scholarship	China	--
Amway (China)	China	--
the Jay and Betty Van Andel Foundation	United States	--
the Ministry of Science and Technology of China	China	2012CB910403
the Ministry of Science and Technology of China	China	2013CB910601
the Ministry of Science and Technology of China	China	XDB08020303