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- PDB-3hve: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -

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Basic information

Entry
Database: PDB / ID: 3hve
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: GigaxoninBTB/3-box
Components(Gigaxonin) x 2
Keywordsprotein binding / ligase / ubiquitin / Gigaxonin / Cytoplasm / Cytoskeleton / Disease mutation / Kelch repeat / Neurodegeneration / Phosphoprotein / Polymorphism / Ubl conjugation / Ubl conjugation pathway
Function / homology
Function and homology information


Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / cytoskeleton organization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / cytoplasm / cytosol
Similarity search - Function
Gigaxonin / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 ...Gigaxonin / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhuang, M. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2009
Title: Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases.
Authors: Zhuang, M. / Calabrese, M.F. / Liu, J. / Waddell, M.B. / Nourse, A. / Hammel, M. / Miller, D.J. / Walden, H. / Duda, D.M. / Seyedin, S.N. / Hoggard, T. / Harper, J.W. / White, K.P. / Schulman, B.A.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2018Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gigaxonin
B: Gigaxonin


Theoretical massNumber of molelcules
Total (without water)57,3472
Polymers57,3472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-15 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.480, 55.600, 120.600
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gigaxonin / Kelch-like protein 16


Mass: 29419.652 Da / Num. of mol.: 1 / Fragment: UNP residues 1-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAN, GAN1, KLHL16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2C0
#2: Protein Gigaxonin / Kelch-like protein 16


Mass: 27927.311 Da / Num. of mol.: 1 / Fragment: UNP residues 1-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAN, GAN1, KLHL16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2C0
Has protein modificationY
Sequence detailsTHE AUTHORS MODELED RESIDUES B165-B210 AS UNK, SINCE THE ELECTRON DENSITY IS POOR IN THIS REGION ...THE AUTHORS MODELED RESIDUES B165-B210 AS UNK, SINCE THE ELECTRON DENSITY IS POOR IN THIS REGION AND THEY DO NOT KNOW WHICH AMINO ACIDS THESE CORRESPOND TO IN TERMS OF THE SEQUENCE. THE ACTUAL CRYSTALLIZED SEQUENCE IN THIS REGION IS SSTEEFLELSPQKLKEVISLEKLNVGNERYVFEAVIRWIAHDTEIR

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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: 2.65 Å3/Da / Density % sol: 53.55 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9794 Å
DetectorDate: Apr 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 15314 / Observed criterion σ(F): 0 / Redundancy: 3.2 % / Rsym value: 0.057 / Net I/σ(I): 20.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 903 / Rsym value: 0.171

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.333 615 -random
Rwork0.3025 ---
all-15429 --
obs-13573 88 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 0 0 3049

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