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- PDB-5fta: Crystal structure of the N-terminal BTB domain of human KCTD10 -

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Basic information

Entry
Database: PDB / ID: 5fta
TitleCrystal structure of the N-terminal BTB domain of human KCTD10
ComponentsBTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3
KeywordsTRANSFERASE
Function / homology
Function and homology information


Notch binding / Cul3-RING ubiquitin ligase complex / negative regulation of Rho protein signal transduction / protein homooligomerization / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1/2/3 / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB domain profile. / 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 adapter for CUL3-mediated RhoA degradation protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsPinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Tallant, C. / Newman, J.A. / Kopec, J. / Fitzpatrick, F. / Talon, R. / Collins, P. ...Pinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Tallant, C. / Newman, J.A. / Kopec, J. / Fitzpatrick, F. / Talon, R. / Collins, P. / Krojer, T. / 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
DepositionJan 12, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 17, 2016ID: 4UES
Revision 1.0Feb 17, 2016Provider: 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 2.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3
B: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3
C: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3
D: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2048
Polymers50,4024
Non-polymers8024
Water57632
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-110.8 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.150, 83.660, 58.680
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3 / HBACURD3 / BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD10 / POTASSIUM CHANNEL TETRAMERIZATION DOMAIN- ...HBACURD3 / BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD10 / POTASSIUM CHANNEL TETRAMERIZATION DOMAIN-CONTAINING PROTEIN 10 / KCTD10


Mass: 12600.397 Da / Num. of mol.: 4 / Fragment: BTB DOMAIN, UNP RESIDUES 26-135 / Mutation: YES
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: Q9H3F6
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.4
Details: 20% PEG3350, 0.1M TRIS PH 8.4, 0.2M MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.64→17.77 Å / Num. obs: 13630 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.1
Reflection shellResolution: 2.64→2.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.64→17.766 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 681 5 %
Rwork0.226 --
obs0.2276 13614 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→17.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 4 32 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033112
X-RAY DIFFRACTIONf_angle_d0.7254210
X-RAY DIFFRACTIONf_dihedral_angle_d10.1521142
X-RAY DIFFRACTIONf_chiral_restr0.029494
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.84310.30431380.27632586X-RAY DIFFRACTION99
2.8431-3.12780.30251330.27572553X-RAY DIFFRACTION100
3.1278-3.57720.31231390.24972574X-RAY DIFFRACTION100
3.5772-4.49480.21881310.21042597X-RAY DIFFRACTION100
4.4948-17.76590.23651400.19752623X-RAY DIFFRACTION99

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