[English] 日本語
Yorodumi
- PDB-5a15: Crystal structure of the BTB domain of human KCTD16 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a15
TitleCrystal structure of the BTB domain of human KCTD16
ComponentsBTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / regulation of G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / presynaptic membrane / postsynaptic membrane / receptor complex / identical protein binding
Similarity search - Function
: / KCTD8/12/16 H1 domain / 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: 2.76 Å
AuthorsPinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Canning, P. / Dixon Clarke, S.E. / Talon, R. / Wiggers, H.J. / Fitzpatrick, F. / Tallant, C. ...Pinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Canning, P. / Dixon Clarke, S.E. / Talon, R. / Wiggers, H.J. / Fitzpatrick, F. / Tallant, C. / Kopec, J. / Chalk, R. / Doutch, J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases.
Authors: Pinkas, D.M. / Sanvitale, C.E. / Bufton, J.C. / Sorrell, F.J. / Solcan, N. / Chalk, R. / Doutch, J. / Bullock, A.N.
History
DepositionApr 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 2.0Dec 6, 2017Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)209,44315
Polymers209,44315
Non-polymers00
Water00
1
A: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.790, 69.370, 134.240
Angle α, β, γ (deg.)102.45, 95.72, 90.71
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD16 / KCTD16 / POTASSIUM CHANNEL TETRAMERIZATION DOMAIN-CONTAINING PROTEIN 16


Mass: 13962.897 Da / Num. of mol.: 15 / Fragment: BTB DOMAIN, UNP RESIDUES 16-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q68DU8

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 % / Description: NONE
Crystal growpH: 6 / Details: 21% PEG3350, 0.1M BIS-TRIS PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.76→36.55 Å / Num. obs: 50928 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 81.92 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.7
Reflection shellResolution: 2.76→2.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UES

4ues
PDB Unreleased entry


Resolution: 2.76→34.65 Å / SU ML: 0.39 / σ(F): 1.96 / Phase error: 33.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 2456 4.8 %
Rwork0.2165 --
obs0.2185 50911 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.9 Å2
Refinement stepCycle: LAST / Resolution: 2.76→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11810 0 0 0 11810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312155
X-RAY DIFFRACTIONf_angle_d0.7916463
X-RAY DIFFRACTIONf_dihedral_angle_d19.7957262
X-RAY DIFFRACTIONf_chiral_restr0.0341764
X-RAY DIFFRACTIONf_plane_restr0.0042109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7601-2.81320.38951290.34112661X-RAY DIFFRACTION98
2.8132-2.87060.37781440.32642727X-RAY DIFFRACTION99
2.8706-2.9330.35671200.29442712X-RAY DIFFRACTION98
2.933-3.00110.30431610.26822679X-RAY DIFFRACTION98
3.0011-3.07620.3251340.27312686X-RAY DIFFRACTION98
3.0762-3.15930.29671380.2742738X-RAY DIFFRACTION98
3.1593-3.25220.34431400.27342714X-RAY DIFFRACTION98
3.2522-3.35710.3691200.25022757X-RAY DIFFRACTION99
3.3571-3.47690.29441080.24312717X-RAY DIFFRACTION98
3.4769-3.6160.26321510.23492716X-RAY DIFFRACTION99
3.616-3.78040.28441310.24392689X-RAY DIFFRACTION98
3.7804-3.97940.28371280.23632705X-RAY DIFFRACTION98
3.9794-4.22830.28451530.21012683X-RAY DIFFRACTION98
4.2283-4.55420.23971420.19092692X-RAY DIFFRACTION98
4.5542-5.01120.22011540.19642684X-RAY DIFFRACTION98
5.0112-5.73350.23581320.20352654X-RAY DIFFRACTION96
5.7335-7.21290.27221240.21492619X-RAY DIFFRACTION95
7.2129-34.65340.20081470.17172622X-RAY DIFFRACTION96

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more