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

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Basic information

Entry
Database: PDB / ID: 6oct
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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


Theoretical massNumber of molelcules
Total (without water)133,66210
Polymers133,66210
Non-polymers00
Water2,432135
1
A: BTB/POZ domain-containing protein KCTD16
B: BTB/POZ domain-containing protein KCTD16
E: BTB/POZ domain-containing protein KCTD16
G: BTB/POZ domain-containing protein KCTD16
H: 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
C: BTB/POZ domain-containing protein KCTD16
D: BTB/POZ domain-containing protein KCTD16
F: 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
Unit cell
Length a, b, c (Å)68.993, 68.993, 261.559
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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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.: 10
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 / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 6
Details: 6% PEG 6000 2% glycerol 0.1 M sodium cacodylate trihydrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→130.78 Å / Num. obs: 34280 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 85.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.057 / Rrim(I) all: 0.131 / Net I/σ(I): 10.5 / Num. measured all: 181942
Reflection shellResolution: 2.8→3.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.74 / Num. unique obs: 9764 / CC1/2: 0.798 / Rpim(I) all: 0.375 / Rrim(I) all: 0.831 / % possible all: 99.6

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Processing

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

6ocr


Resolution: 2.8→37.91 Å / Cor.coef. Fo:Fc: 0.9037 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 1.504 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.94 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.326
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1713 5.01 %RANDOM
Rwork0.2272 ---
obs0.2278 34193 99.73 %-
Displacement parametersBiso max: 172.17 Å2 / Biso mean: 84.1 Å2 / Biso min: 31.07 Å2
Baniso -1Baniso -2Baniso -3
1-11.9074 Å20 Å20 Å2
2--11.9074 Å20 Å2
3----23.8148 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 2.8→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8047 0 0 135 8182
Biso mean---58.45 -
Num. residues----957
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2880SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1187HARMONIC5
X-RAY DIFFRACTIONt_it8268HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion972SEMIHARMONIC5
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_contact8825SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8268HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg11151HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion17.19
LS refinement shellResolution: 2.8→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3076 168 5.7 %
Rwork0.2591 2778 -
all0.2619 2946 -
obs--99.73 %
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)
1-0.55010.7632-0.10671.3-0.14170-0.0079-0.0006-0.00120.00140.0118-0.00750.0031-0.0137-0.00390.0723-0.0746-0.0101-0.0744-0.0077-0.0007106.961136.6842-14.7167
20.03640.33460.05880.37470.10030.212-0.00950.006-0.00690.00630.0049-0.0029-0.00860.00960.00460.0535-0.0522-0.0045-0.05930.00380.0017133.9453162.582-7.8487
3-0.12940.60680.22330.74380.50660.0423-0.0006-0.0012-0.007-0.00210.0075-0.00710.0004-0.0028-0.00690.0446-0.0637-0.0136-0.0408-0.0118-0.006291.2285125.8776-34.2643
4-0.11740.27260.22310.35390.25120.21760.0010.0027-0.0012-0.00450.0027-0.0014-0.0013-0.0043-0.00370.0378-0.0472-0.0105-0.02790.0042-0.010376.9361117.0468-48.4585
5-0.20610.26750.36590.4268-0.13740.1078-0.0006-0.0086-0.0020.00480.0045-0.00660.00010.0012-0.00390.0385-0.0348-0.0348-0.0392-0.0093-0.0006113.6709125.33222.9507
6-0.08870.4696-0.03160.5718-0.09880.0073-0.00210.0035-0.003-0.00420.0057-0.0043-0.0046-0.0035-0.00360.0504-0.0682-0.0069-0.04650.0069-0.007496.8908147.0222-36.4051
7-0.19840.0705-0.13160.3508-0.32040.5335-0.0001-0.0052-0.00170.00460.00120.0003-0.00070.0027-0.00110.037-0.00740.0039-0.02370.0101-0.0056135.3979155.68212.9895
8-0.17010.7075-0.00060.87370.38180.0186-0.00970.0078-0.0016-0.00010.0088-0.0023-0.0083-0.00370.00090.0628-0.0663-0.0094-0.0652-0.01840.0008118.3496154.4944-21.0575
9-0.00780.11060.32350.13030.03340.2876-0.00230.0036-0.0045-0.00190.00280.005-0.0055-0.0048-0.00050.027-0.0306-0.0182-0.01220.0006-0.011589.8326158.6914-53.928
100.14150.06510.21190.3718-0.14770.3126-0.00010.0010.0016-0.0008-0.00010.0032-0.0007-0.00070.00020.0188-0.006-0.01270.00750.01360.005865.1147130.5881-61.3231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A22 - 124
2X-RAY DIFFRACTION2{ B|* }B22 - 124
3X-RAY DIFFRACTION3{ C|* }C22 - 123
4X-RAY DIFFRACTION4{ D|* }D22 - 124
5X-RAY DIFFRACTION5{ E|* }E22 - 124
6X-RAY DIFFRACTION6{ F|* }F22 - 124
7X-RAY DIFFRACTION7{ G|* }G22 - 123
8X-RAY DIFFRACTION8{ H|* }H22 - 124
9X-RAY DIFFRACTION9{ I|* }I23 - 123
10X-RAY DIFFRACTION10{ J|* }J22 - 123

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