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9JKQ:
Cryo-EM structure of the METH-bound hTAAR1-Gs complex
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PDB ID:
9JKQ
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MMDB ID:
253808
PDB Deposition Date:
2024/9/16
Updated in MMDB:
2024/10
Experimental Method:
electron microscopy
Resolution:
2.66 Å
Source Organism:
synthetic construct
▼
Taxonomy
Molecule
synthetic construct
R
Homo sapiens
A, B, C, N
Similar Structures:
VAST+
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Biological Unit
Asymmetric Unit
Biological Unit for 9JKQ: pentameric; determined by author and by software
Molecular Graphic
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Interactions
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A
A: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
B
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N
N: Nb35
R
R: Soluble cytochrome b562,Trace amine-associated receptor 1
1
B40: (2S)-N-methyl-1-phenylpropan-2-amine
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Protein
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Chemical
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Format:
ASN.1 (Cn3D)
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PNG (image)
Data Set:
alpha-Carbons
Single 3D structure
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Molecular Components in 9JKQ
Label
Count
Molecule
Proteins (5 molecules)
A
1
Guanine Nucleotide-binding Protein G(s) Subunit Alpha Isoforms Short
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
100
200
300
394
394 residues, click to see VAST similar structures.
helix 10-39
helix 265-278
helix 294-302
helix 332-349
helix 370-391
strand 40-47
strand 206-215
strand 216-225
strand 242-250
strand 284-293
strand 356-365
Domain 1 (40-394): click to see VAST similar structures
1
GTP/Mg2+ binding site
GTP/Mg2+ binding(12)
location: 47, residue: G
location: 52, residue: G
location: 53, residue: K
location: 54, residue: N
location: 204, residue: T
location: 223, residue: D
location: 226, residue: A
location: 292, residue: N
location: 293, residue: K
location: 295, residue: D
location: 365, residue: C
location: 366, residue: A
adenylyl cyclase interaction site
adenylyl cyclase interaction site(5)
location: 207, residue: I
location: 232, residue: R
location: 235, residue: I
location: 236, residue: Q
location: 239, residue: N
beta - gamma complex interaction site
beta - gamma complex interaction site(15)
location: 205, residue: S
location: 207, residue: I
location: 209, residue: E
location: 220, residue: H
location: 222, residue: F
location: 226, residue: A
location: 227, residue: Q
location: 228, residue: R
location: 230, residue: E
location: 233, residue: K
location: 234, residue: W
location: 236, residue: Q
location: 237, residue: C
location: 238, residue: F
location: 239, residue: N
GoLoco binding site
GoLoco binding site(16)
location: 48, residue: A
location: 49, residue: G
location: 50, residue: E
location: 93, residue: Q
location: 97, residue: N
location: 101, residue: E
location: 104, residue: E
location: 107, residue: V
location: 108, residue: A
location: 128, residue: V
location: 131, residue: I
location: 172, residue: I
location: 201, residue: R
location: 226, residue: A
location: 234, residue: W
location: 238, residue: F
putative receptor binding site
putative receptor binding site(16)
location: 357, residue: H
location: 358, residue: Y
location: 359, residue: C
location: 360, residue: Y
location: 361, residue: P
location: 362, residue: H
location: 363, residue: F
location: 364, residue: T
location: 365, residue: C
location: 366, residue: A
location: 367, residue: V
location: 368, residue: D
location: 370, residue: E
location: 371, residue: N
location: 372, residue: I
location: 373, residue: R
Switch I region
Switch I region(9)
location: 199, residue: R
location: 200, residue: C
location: 201, residue: R
location: 202, residue: V
location: 203, residue: L
location: 204, residue: T
location: 205, residue: S
location: 206, residue: G
location: 207, residue: I
Switch II region
Switch II region(17)
location: 224, residue: V
location: 225, residue: G
location: 226, residue: A
location: 227, residue: Q
location: 228, residue: R
location: 229, residue: D
location: 230, residue: E
location: 231, residue: R
location: 232, residue: R
location: 233, residue: K
location: 234, residue: W
location: 235, residue: I
location: 236, residue: Q
location: 237, residue: C
location: 238, residue: F
location: 239, residue: N
location: 240, residue: D
G1 box
G1 box(8)
location: 47, residue: G
location: 48, residue: A
location: 49, residue: G
location: 50, residue: E
location: 51, residue: S
location: 52, residue: G
location: 53, residue: K
location: 54, residue: N
G2 box
G2 box(1)
location: 204, residue: T
G3 box
G3 box(4)
location: 223, residue: D
location: 224, residue: V
location: 225, residue: G
location: 226, residue: A
G4 box
G4 box(4)
location: 292, residue: N
location: 293, residue: K
location: 294, residue: Q
location: 295, residue: D
G5 box
G5 box(3)
location: 365, residue: C
location: 366, residue: A
location: 367, residue: V
G-alpha
cd00066 (41-388): Alpha subunit of G proteins (guanine nucleotide binding)
P-loop_NTPase superfamily
cl38936(41-388): Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A...
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B
1
Guanine Nucleotide-binding Protein G(i)/g(s)/g(t) Subunit Beta-1
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
100
200
300
351
351 residues, click to see VAST similar structures.
helix 17-36
strand 57-63
strand 67-75
strand 79-87
strand 88-95
strand 98-106
strand 110-117
strand 121-128
strand 131-137
strand 144-151
strand 155-164
strand 166-174
strand 175-183
strand 184-192
strand 197-204
strand 208-215
strand 217-225
strand 226-234
strand 238-246
strand 250-258
strand 259-266
strand 269-276
strand 283-290
strand 294-301
strand 303-310
strand 313-320
strand 325-332
strand 337-343
strand 345-351
Domain 1 (47-194): click to see VAST similar structures
1
Domain 2 (195-322): click to see VAST similar structures
2
Domain 1 (323-351): click to see VAST similar structures
1
structural tetrad
structural tetrad(40)
location: 65, residue: H
location: 83, residue: S
location: 87, residue: D
location: 93, residue: W
location: 94, residue: D
location: 101, residue: V
location: 102, residue: H
location: 125, residue: C
location: 129, residue: D
location: 135, residue: Y
location: 136, residue: N
location: 152, residue: G
location: 153, residue: H
location: 170, residue: T
location: 174, residue: D
location: 180, residue: W
location: 181, residue: D
location: 194, residue: H
location: 211, residue: V
location: 216, residue: D
location: 222, residue: W
location: 223, residue: D
location: 235, residue: G
location: 236, residue: H
location: 254, residue: T
location: 258, residue: D
location: 264, residue: F
location: 265, residue: D
location: 276, residue: S
location: 277, residue: H
location: 297, residue: L
location: 302, residue: D
location: 308, residue: W
location: 309, residue: D
location: 321, residue: G
location: 322, residue: H
location: 340, residue: T
location: 344, residue: D
location: 350, residue: W
location: 351, residue: N
WD40
cd00200 (59-351): WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly
WD40 superfamily
cl29593(59-351): WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal...
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C
1
Guanine Nucleotide-binding Protein G(i)/g(s)/g(o) Subunit Gamma-2
1 Protein
SS Diagram
Features
Domain Families
Specific Hits
Super Families
1
50
71
71 residues, click to see VAST similar structures.
helix 11-22
helix 30-44
beta subunit binding site
beta subunit binding site(15)
location: 9, residue: I
location: 12, residue: A
location: 16, residue: V
location: 19, residue: L
location: 23, residue: A
location: 28, residue: I
location: 30, residue: V
location: 33, residue: A
location: 34, residue: A
location: 37, residue: L
location: 38, residue: M
location: 41, residue: C
location: 50, residue: L
location: 51, residue: L
location: 61, residue: F
GGL
smart00224 (9-71): G protein gamma subunit-like motifs
GGL
cl00069(9-71): G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G...
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N
1
Nb35
1 Protein
SS Diagram
Features
Domain Families
Specific Hits
Super Families
1
100
162
162 residues, click to see VAST similar structures.
strand 26-32
strand 33-38
strand 39-50
strand 56-64
strand 69-77
strand 81-85
strand 91-99
strand 100-111
strand 115-123
strand 145-151
heterodimer interface
heterodimer interface(6)
location: 63, residue: Q
location: 67, residue: K
location: 71, residue: W
location: 119, residue: Y
location: 142, residue: R
location: 143, residue: G
antigen binding site
antigen binding site(3)
location: 57, residue: K
location: 74, residue: D
location: 123, residue: C
intrachain IgC domain interface
intrachain IgC domain interface(5)
location: 33, residue: G
location: 35, residue: L
location: 147, residue: Q
location: 149, residue: T
location: 151, residue: S
IgV_H
cd04981 (27-151): Immunoglobulin (Ig) heavy chain (H), variable (V) domain
Ig superfamily
cl11960(27-151): The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins,...
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R
1
Soluble Cytochrome B562,trace Amine-associated Receptor 1
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
100
200
300
400
510
510 residues, click to see VAST similar structures.
helix 145-174
helix 182-199
helix 203-211
helix 219-251
helix 263-286
helix 295-304
helix 313-323
helix 326-354
helix 374-388
helix 389-398
helix 408-419
helix 435-447
Domain 1 (1-290): click to see VAST similar structures
1
Domain 2 (309-427): click to see VAST similar structures
2
putative ligand binding site
putative ligand binding site(17)
location: 224, residue: H
location: 228, residue: D
location: 229, residue: I
location: 232, residue: S
location: 233, residue: S
location: 309, residue: V
location: 316, residue: G
location: 319, residue: T
location: 320, residue: F
location: 323, residue: S
location: 389, residue: W
location: 392, residue: F
location: 393, residue: F
location: 396, residue: T
location: 411, residue: N
location: 415, residue: I
location: 419, residue: Y
PRK15058
PRK15058 (2-124): cytochrome b562
Cytochrom_B562
cl01546(2-124): This family contains the bacterial cytochrome b562. This forms a four-helix bundle that non-covalently binds a single heme prosthetic group..
7tmA_TAAR1
cd15314 (151-440): trace amine-associated receptor 1 and similar receptors, member of the class A family of seven-transmembrane G protein-coupled receptors
7tm_GPCRs superfamily
cl28897(151-440): This hierarchical evolutionary model represents the seven-transmembrane (7TM) receptors, often referred to as G protein-coupled receptors (GPCRs),...
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Chemical and Non-standard biopolymers (1 molecule)
1
1
(2S)-N-methyl-1-phenylpropan-2-amine
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Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.
"
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
Nucleic Acids Res. 2014 Jan; 42(Database issue)
:D297-303
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