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- PDB-6ocp: Crystal structure of a human GABAB receptor peptide bound to KCTD16 T1 -

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Basic information

Entry
Database: PDB / ID: 6ocp
TitleCrystal structure of a human GABAB receptor peptide bound to KCTD16 T1
Components
  • BTB/POZ domain-containing protein KCTD16
  • Gamma-aminobutyric acid type B receptor subunit 2
KeywordsSIGNALING PROTEIN / KCTD16 / Pentamer / Complex / GABA(B) receptor
Function / homology
Function and homology information


GABA B receptor activation / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / regulation of G protein-coupled receptor signaling pathway / gamma-aminobutyric acid signaling pathway ...GABA B receptor activation / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / regulation of G protein-coupled receptor signaling pathway / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / transmembrane signaling receptor activity / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / receptor complex / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / GPCR family 3, GABA-B receptor / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal ...GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / GPCR family 3, GABA-B receptor / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid type B receptor subunit 2 / BTB/POZ domain-containing protein KCTD16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZuo, H. / Glaaser, I. / Zhao, Y. / Kurinov, I. / Mosyak, L. / Wang, H. / Liu, J. / Park, J. / Frangaj, A. / Sturchler, E. ...Zuo, H. / Glaaser, I. / Zhao, Y. / Kurinov, I. / Mosyak, L. / Wang, H. / Liu, J. / Park, J. / Frangaj, A. / Sturchler, E. / Zhou, M. / McDonald, P. / Geng, Y. / Slesinger, P.A. / Fan, Q.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM088454 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125801 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA037170 United States
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)R01AA018734 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural basis for auxiliary subunit KCTD16 regulation of the GABABreceptor.
Authors: Zuo, H. / Glaaser, I. / Zhao, Y. / Kurinov, I. / Mosyak, L. / Wang, H. / Liu, J. / Park, J. / Frangaj, A. / Sturchler, E. / Zhou, M. / McDonald, P. / Geng, Y. / Slesinger, P.A. / Fan, Q.R.
History
DepositionMar 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BTB/POZ domain-containing protein KCTD16
B: BTB/POZ domain-containing protein KCTD16
C: BTB/POZ domain-containing protein KCTD16
D: BTB/POZ domain-containing protein KCTD16
E: BTB/POZ domain-containing protein KCTD16
F: BTB/POZ domain-containing protein KCTD16
G: BTB/POZ domain-containing protein KCTD16
H: BTB/POZ domain-containing protein KCTD16
I: BTB/POZ domain-containing protein KCTD16
J: BTB/POZ domain-containing protein KCTD16
K: BTB/POZ domain-containing protein KCTD16
L: BTB/POZ domain-containing protein KCTD16
M: BTB/POZ domain-containing protein KCTD16
N: BTB/POZ domain-containing protein KCTD16
O: BTB/POZ domain-containing protein KCTD16
P: Gamma-aminobutyric acid type B receptor subunit 2
Q: Gamma-aminobutyric acid type B receptor subunit 2
R: Gamma-aminobutyric acid type B receptor subunit 2


Theoretical massNumber of molelcules
Total (without water)205,34718
Polymers205,34718
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.792, 69.105, 137.889
Angle α, β, γ (deg.)102.190, 94.830, 91.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
BTB/POZ domain-containing protein KCTD16 / Potassium channel tetramerization domain-containing protein 16


Mass: 13366.242 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD16, KIAA1317 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codonplus RIL / References: UniProt: Q68DU8
#2: Protein/peptide Gamma-aminobutyric acid type B receptor subunit 2 / Gb2 / G-protein coupled receptor 51 / HG20


Mass: 1617.889 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75899
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2% PEG 6000 2% glycerol 8% PEG 400 0.1 M sodium cacodylate trihydrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→67.11 Å / Num. obs: 77129 / % possible obs: 90.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 66.27 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.07 / Net I/σ(I): 7.4 / Num. measured all: 149442
Reflection shellResolution: 2.35→2.71 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.296 / Num. unique obs: 26932 / CC1/2: 0.92 / Rpim(I) all: 0.296 / Rrim(I) all: 0.418 / % possible all: 90.3

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
BUSTER2.11.5refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OCR

6ocr


Resolution: 2.35→67.11 Å / Cor.coef. Fo:Fc: 0.9053 / Cor.coef. Fo:Fc free: 0.9032 / SU R Cruickshank DPI: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.333 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 3798 4.92 %RANDOM
Rwork0.2216 ---
obs0.2225 77122 90.69 %-
Displacement parametersBiso max: 192.29 Å2 / Biso mean: 90.08 Å2 / Biso min: 42.47 Å2
Baniso -1Baniso -2Baniso -3
1--40.9137 Å28.4888 Å2-14.9843 Å2
2--25.9587 Å25.4327 Å2
3---14.955 Å2
Refine analyzeLuzzati coordinate error obs: 0.404 Å
Refinement stepCycle: final / Resolution: 2.35→67.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12331 0 0 230 12561
Biso mean---79.74 -
Num. residues----1466
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4399SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes248HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1817HARMONIC5
X-RAY DIFFRACTIONt_it12676HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1497SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13777SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12676HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg17100HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion15.74
LS refinement shellResolution: 2.35→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2774 272 4.72 %
Rwork0.2507 5489 -
all0.2519 5761 -
obs--90.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02790.2681-0.21840.08020.19310.0325-0.00140.00290.006-0.0018-0.00270.0031-0.0032-0.00240.0041-0.0009-0.02070.0175-0.0003-0.0195-0.009534.806340.6398-3.1551
20.01780.061-0.0302-0.14070.3140.21130.0008-0.00550.00540.0064-0.00220.00720.003-0.00680.0013-0.0068-0.01910.02110.0032-0.0267-0.021913.30858.8143-24.7951
30.02540.21430.00170.00380.18280.0732-0.0016-0.00060.00130.0038-0.0012-0.00220.00150.0030.0027-0.0032-0.02020.0122-0.0029-0.0094-0.002450.798345.917210.896
40.38910.7004-1.77642.5744-0.39041.6833-0.00150.01810.0139-0.00320.00130.05110.002-0.04440.0002-0.0150.0232-0.0074-0.03150.0125019.64344.1033-45.5951
50.16660.4-0.24020.62160.19960.71580.0007-0.0066-0.00770.00560.0014-0.0190.00440.0208-0.00210.0140.0017-0.00740.02980.00010.025318.65628.0315-45.4115
6-0.0151-0.13850.27850.22050.05140.0655-0.0013-0.00460.0002-0.01540.0003-0.0002-0.00120.00850.001-0.01540.0449-0.0325-0.04530.0244-0.007829.872119.2105-57.8217
70.0527-0.130.21290.3753-0.1266-0.03120.0027-0.0051-0.0001-0.00710.00240.0029-0.0120.0136-0.0051-0.01380.0277-0.0369-0.04320.0263-0.00729.845540.3084-52.0454
80.30940.7551-0.62690.69090.12390.4173-0.0005-0.00530.00580.004-0.00010.0253-0.0011-0.01080.0006-0.00070.0155-0.0023-0.01580.02810.006517.676846.5429-34.8669
90.05740.1106-0.3132-0.0650.14820.0984-0.00010.00180.0012-0.00520.0001-0.0032-0.00090.00530-0.0068-0.00850.00870.0061-0.0078-0.010857.242430.6036-89.9112
100.07590.1382-0.16620.04490.09580.085-0.0002-0.0035-0.0035-0.00750.00440.0011-0.00510.01-0.0043-0.0163-0.0111-0.003-0.01810.0071-0.008944.522436.494-73.046
11-0.00610.12030.01810.3554-0.3082-0.1250.0017-0.00050.0053-0.00230.00530.0041-0.00940.004-0.0070.0103-0.00480.0107-0.03280.0203-0.002738.887757.6605-71.5399
120.2940.3932-0.32810.1684-0.02250.23870-0.0044-0.01070.0013-0.0001-0.00560.00690.00290.00010.013200.0116-0.01150.01110.006747.056172.4301-85.4303
130.0423-0.115-0.06-0.060.10870.06530-0.0005-0.00140.0002-0.0005-0.00480.0020.00390.0006-0.00070.00170.00490.0037-0.0074-0.00964.428267.0498-97.6783
140.11590.2510.0452-0.0360.12550.05410.0002-0.0015-0.0040.0016-0.0002-0.00310.00160.00010-0.005-0.02670.00450.0065-0.011-0.010657.06988.631413.6283
150.07920.3916-0.0658-0.01530.11420.0780.0016-0.0039-0.0069-0.00070.00320.00180.0001-0.0006-0.0047-0.0039-0.04170.01330.0052-0.0157-0.014537.38253.91525.9305
160.12350.5163-0.2336-0.16540.49030.1615-0.0001-0.00140.0007-0.0023-0.00020.0062-0.0022-0.00060.0002-0.0063-0.03490.03860.0171-0.0541-0.031326.811120.2787-4.0889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ N|* }N23 - 123
2X-RAY DIFFRACTION2{ A|* }A23 - 124
3X-RAY DIFFRACTION3{ O|* }O23 - 123
4X-RAY DIFFRACTION4{ B|* }B23 - 126
5X-RAY DIFFRACTION5{ P|* }P895 - 909
6X-RAY DIFFRACTION6{ C|* }C23 - 123
7X-RAY DIFFRACTION7{ D|* }D22 - 124
8X-RAY DIFFRACTION8{ E|* }E22 - 124
9X-RAY DIFFRACTION9{ F|* }F23 - 123
10X-RAY DIFFRACTION10{ G|* }G22 - 125
11X-RAY DIFFRACTION11{ H|* }H23 - 123
12X-RAY DIFFRACTION12{ I|* }I23 - 123
13X-RAY DIFFRACTION13{ J|* }J23 - 123
14X-RAY DIFFRACTION14{ K|* }K22 - 123
15X-RAY DIFFRACTION15{ L|* }L22 - 124
16X-RAY DIFFRACTION16{ M|* }M23 - 123

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