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- PDB-6ocr: Crystal structure of human KCTD16 T1 domain -

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Basic information

Entry
Database: PDB / ID: 6ocr
TitleCrystal structure of human KCTD16 T1 domain
ComponentsBTB/POZ domain-containing protein KCTD16
KeywordsSIGNALING PROTEIN / KCTD16 / Pentamer / GABA(B) receptor
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / presynaptic membrane / postsynaptic membrane / receptor complex
Similarity search - Function
: / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BTB/POZ domain-containing protein KCTD16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.28 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 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)200,49415
Polymers200,49415
Non-polymers00
Water3,711206
1
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


Theoretical massNumber of molelcules
Total (without water)66,8315
Polymers66,8315
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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


Theoretical massNumber of molelcules
Total (without water)66,8315
Polymers66,8315
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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


Theoretical massNumber of molelcules
Total (without water)66,8315
Polymers66,8315
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.139, 68.646, 131.679
Angle α, β, γ (deg.)102.110, 97.980, 89.880
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 7 / Details: 20% ethanol, 0.1 M Tris, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→220 Å / Num. obs: 78702 / % possible obs: 92 % / Redundancy: 1.9 % / Biso Wilson estimate: 65.67 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.06 / Net I/σ(I): 13.1 / Num. measured all: 152071
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.25-2.331.60.61734170.906140
2.33-2.421.80.50579620.867192.7
2.42-2.531.90.37784150.918197.8
2.53-2.6720.25983410.98198
2.67-2.8320.1683681.006198.3
2.83-3.0520.09784230.996198.5
3.05-3.3620.06584671.132198.7
3.36-3.8520.04484541.242198.9
3.85-4.8520.03685071.195199.1
4.85-2201.90.02383481.204198

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.28→41.97 Å / Cor.coef. Fo:Fc: 0.9181 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.344 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 3981 5.06 %RANDOM
Rwork0.2538 ---
obs0.2546 78696 95.82 %-
Displacement parametersBiso max: 177.99 Å2 / Biso mean: 79.14 Å2 / Biso min: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1--11.4452 Å212.6774 Å2-2.9021 Å2
2--9.3518 Å26.1227 Å2
3---2.0934 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.28→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12095 0 0 206 12301
Biso mean---64.09 -
Num. residues----1435
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4345SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes252HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1782HARMONIC5
X-RAY DIFFRACTIONt_it12428HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1463SEMIHARMONIC5
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_contact13764SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12428HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16756HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion15.94
LS refinement shellResolution: 2.28→2.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2414 192 4.58 %
Rwork0.234 4004 -
all0.2344 4196 -
obs--95.82 %
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)
10.0157-0.6058-0.0610.78970.13270.04150.0015-0.0073-0.012-0.01080.0035-0.0028-0.00820.0047-0.0050.03220.03030.0149-0.06880.03470.0054-8.7348-34.828160.3481
20.2010.1921-0.277-0.03880.07880.28070.0006-0.0028-0.00440.00080.0003-0.00460.00390.0046-0.00090.0078-0.03890.01770.017-0.024-0.0255-21.7943-9.438519.4478
30.0852-0.0981-0.32280.2662-0.37240.317-0.0001-0.0092-0.00710.0071-0.00080.0090.0061-0.00130.00090.00950.01680.0088-0.01370.0392-0.0079-21.7892-28.101376.8555
40.10250.6391-0.35130.421-0.39460.0178-0.0010.00090.00550.00150.0019-0.00160.00760.0015-0.00090.0263-0.04880.033-0.0258-0.0024-0.0101-40.3554-2.900429.6514
50.06770.679-0.23080.7415-0.6150.04040.00080.00220.0066-0.00360.01090.0092-0.0062-0.0023-0.01170.0527-0.04830.0531-0.06410.0346-0.0051-50.692-17.692942.1031
60.06050.2411-0.21510.46390.11990.1068-0.00320.0033-0.0087-0.00230.0052-0.0052-0.00210.0081-0.00190.0242-0.03830.0588-0.0482-0.0030.0032-45.4024-38.933940.4498
70.62361.0353-0.64050.80990.34530.72450.0004-0.0027-0.01340.0047-0.0071-0.01980.00320.02010.0067-0.0008-0.03550.02410.0294-0.01480.0195-29.0342-45.443326.301
80.1210.15580.3887-0.0110.33050.595-0.00210.00080.00330.0125-0.004-0.0038-0.003-0.00040.0061-0.0058-0.0216-0.01270.0074-0.0105-0.0093-22.3498-0.7452-6.7217
90.28370.20040.2129-0.19730.47320.2569-0.00170.00650.0066-0.0011-0.00170.0079-0.0069-0.00020.0034-0.0201-0.0109-0.01190.0211-0.0444-0.0069-38.5313-5.3226-20.8498
100.62840.27560.2108-0.41720.97370.47250.0020.00110.001-0.00240.0010.0074-0.00380.0035-0.003-0.0421-0.01460.00490.0637-0.102-0.0389-47.2974-25.6899-21.0861
110.40170.09530.2095-0.10870.24270.29320.002-0.0038-0.00590.00510.00050.00170.0045-0.0006-0.0025-0.0256-0.0282-0.01740.0481-0.0291-0.0298-36.7369-42.2903-11.5211
120.9045-0.29330.1639-0.20040.45040.60740.0010.01030.0136-0.0014-0.0016-0.0118-0.0067-0.00090.0006-0.0011-0.0055-0.01230.0483-0.00130.0012-16.9557-39.064-3.5819
130.3124-0.2947-0.0203-0.35540.71780.7430.0016-0.00660.00460.0069-0.00080.0075-0.0026-0.0022-0.0008-0.04020.0128-0.00770.0473-0.0537-0.0223-25.9494-64.732586.0841
140.17-0.2490.00530.2938-0.24110.5181-0.0027-0.00880.0094-0.0150.0019-0.00390.0057-0.00260.0008-0.00320.0429-0.0171-0.01350.0059-0.012-19.413-70.672966.0799
15-0.04930.27870.19021.0253-0.4518-0.2053-0.0071-0.00970.0063-0.02010.0029-0.00450.00070.00210.00420.02190.0090.0181-0.08270.03830.0383-8.7442-55.683654.2094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ N|* }N22 - 124
2X-RAY DIFFRACTION2{ A|* }A23 - 123
3X-RAY DIFFRACTION3{ O|* }O23 - 123
4X-RAY DIFFRACTION4{ B|* }B23 - 123
5X-RAY DIFFRACTION5{ C|* }C23 - 123
6X-RAY DIFFRACTION6{ D|* }D22 - 126
7X-RAY DIFFRACTION7{ E|* }E22 - 123
8X-RAY DIFFRACTION8{ F|* }F23 - 124
9X-RAY DIFFRACTION9{ G|* }G23 - 124
10X-RAY DIFFRACTION10{ H|* }H23 - 123
11X-RAY DIFFRACTION11{ I|* }I23 - 124
12X-RAY DIFFRACTION12{ J|* }J23 - 123
13X-RAY DIFFRACTION13{ K|* }K22 - 123
14X-RAY DIFFRACTION14{ L|* }L23 - 123
15X-RAY DIFFRACTION15{ M|* }M22 - 124

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