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- PDB-4uij: Crystal structure of the BTB domain of KCTD13 -

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Basic information

Entry
Database: PDB / ID: 4uij
TitleCrystal structure of the BTB domain of KCTD13
ComponentsBTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


RND2 GTPase cycle / RND3 GTPase cycle / Cul3-RING ubiquitin ligase complex / stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of synaptic transmission / positive regulation of DNA replication / protein homooligomerization / small GTPase binding / cell migration ...RND2 GTPase cycle / RND3 GTPase cycle / Cul3-RING ubiquitin ligase complex / stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of synaptic transmission / positive regulation of DNA replication / protein homooligomerization / small GTPase binding / cell migration / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear body / protein domain specific binding / 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 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPinkas, D.M. / Sanvitale, C.E. / Sorell, F.J. / Solcan, N. / Goubin, S. / Canning, P. / Williams, E. / Chaikuad, A. / Dixon Clarke, S.E. / Tallant, C. ...Pinkas, D.M. / Sanvitale, C.E. / Sorell, F.J. / Solcan, N. / Goubin, S. / Canning, P. / Williams, E. / Chaikuad, A. / Dixon Clarke, S.E. / Tallant, C. / Fonseca, M. / 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
DepositionMar 30, 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 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_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 1
B: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
C: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
D: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0058
Polymers62,8634
Non-polymers1424
Water61334
1
A: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7512
Polymers15,7161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7512
Polymers15,7161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7512
Polymers15,7161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7512
Polymers15,7161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.450, 58.830, 87.170
Angle α, β, γ (deg.)90.00, 105.41, 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 1 / HBACURD1 / BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD13 / POLYMER ASE DELTA-INTERACTING PROTEIN 1 / ...HBACURD1 / BTB/POZ DOMAIN-CONTAINING PROTEIN KCTD13 / POLYMER ASE DELTA-INTERACTING PROTEIN 1 / TNFAIP1-LIKE PROTEIN / KCTD13


Mass: 15715.845 Da / Num. of mol.: 4 / Fragment: BTB DOMAIN, UNP RESIDUES 27-144
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: Q8WZ19
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.94 Å3/Da / Density % sol: 36.74 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.6M MAGNESIUM SULFATE, 0.1M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→37.42 Å / Num. obs: 13431 / % possible obs: 99.8 % / Observed criterion σ(I): -1 / Redundancy: 5 % / Biso Wilson estimate: 57.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / % possible all: 99.8

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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: 2.7→37.417 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2787 714 5.3 %
Rwork0.2349 --
obs0.2373 13409 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→37.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 4 34 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033200
X-RAY DIFFRACTIONf_angle_d0.6194327
X-RAY DIFFRACTIONf_dihedral_angle_d11.5181165
X-RAY DIFFRACTIONf_chiral_restr0.027502
X-RAY DIFFRACTIONf_plane_restr0.002549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.90850.34121580.2972490X-RAY DIFFRACTION100
2.9085-3.2010.31751300.2732527X-RAY DIFFRACTION100
3.201-3.66380.25671350.24182539X-RAY DIFFRACTION100
3.6638-4.61470.29581430.20872532X-RAY DIFFRACTION100
4.6147-37.42070.24891480.22812607X-RAY DIFFRACTION100

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