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

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Basic information

Entry
Database: PDB / ID: 3htm
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box
ComponentsSpeckle-type POZ protein
KeywordsPROTEIN BINDING / ligase / BTB / SPOP / ubiquitin / Nucleus / Ubl conjugation pathway
Function / homology
Function and homology information


molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of proteolysis / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding ...molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of proteolysis / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3030 / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Potassium Channel Kv1.1; Chain A ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3030 / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhuang, M. / Walden, H. / 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 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Speckle-type POZ protein
B: Speckle-type POZ protein
C: Speckle-type POZ protein
D: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)77,1834
Polymers77,1834
Non-polymers00
Water6,053336
1
A: Speckle-type POZ protein
B: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)38,5912
Polymers38,5912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area16390 Å2
MethodPISA
2
C: Speckle-type POZ protein
D: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)38,5912
Polymers38,5912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-22 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.800, 88.700, 88.700
Angle α, β, γ (deg.)90.80, 89.30, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 19295.625 Da / Num. of mol.: 4 / Fragment: UNP residues 172-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorDate: Apr 20, 2005
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 37547 / Observed criterion σ(F): 0 / Redundancy: 1.9 % / Rsym value: 0.065 / Net I/σ(I): 25.5
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.335

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.34 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.256 --
Rwork0.217 --
obs0.217 37547 96.9 %
all-38756 -
Refinement stepCycle: LAST / Resolution: 2.5→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 0 336 5092

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