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- PDB-2oxq: Structure of the UbcH5 :CHIP U-box complex -

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Basic information

Entry
Database: PDB / ID: 2oxq
TitleStructure of the UbcH5 :CHIP U-box complex
Components
  • STIP1 homology and U-Box containing protein 1
  • Ubiquitin-conjugating enzyme E2D 1
KeywordsLIGASE / protein-protein complex
Function / homology
Function and homology information


Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / : / : / : / : / : / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Regulation of APC/C activators between G1/S and early anaphase / : / : ...Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / : / : / : / : / : / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Regulation of APC/C activators between G1/S and early anaphase / : / : / Signaling by BMP / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Senescence-Associated Secretory Phenotype (SASP) / CDK-mediated phosphorylation and removal of Cdc6 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Peroxisomal protein import / Antigen processing: Ubiquitination & Proteasome degradation / : / : / : / Ovarian tumor domain proteases / Neddylation / cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / ubiquitin ligase complex / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / Z disc / protein polyubiquitination / ubiquitin protein ligase activity / protein-folding chaperone binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast) / RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXu, Z. / Nix, J.C. / Devlin, K.I. / Misra, S.
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes.
Authors: Xu, Z. / Kohli, E. / Devlin, K.I. / Bold, M. / Nix, J.C. / Misra, S.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2D 1
B: Ubiquitin-conjugating enzyme E2D 1
C: STIP1 homology and U-Box containing protein 1
D: STIP1 homology and U-Box containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3387
Polymers52,2324
Non-polymers1063
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.042, 93.399, 144.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2D 1 / UBC4/5 homolog / yeast


Mass: 17057.529 Da / Num. of mol.: 2 / Fragment: UbcH5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ube2d1 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3) / References: UniProt: Q6PC58, ubiquitin-protein ligase
#2: Protein STIP1 homology and U-Box containing protein 1


Mass: 9058.354 Da / Num. of mol.: 2 / Fragment: U-box domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: stub1 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q7ZTZ6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.09 Å3/Da / Density % sol: 75.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.65M Ammonium Sulfate, 0.09M Bistris, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 7, 2006
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.9→55 Å / Num. all: 24307 / Num. obs: 24283 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 3.4 % / Biso Wilson estimate: 85.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2387 / Rsym value: 0.466 / % possible all: 100

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Processing

Software
NameClassification
d*TREKdata scaling
CNSrefinement
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F42, 2esk

2f42

2esk


Resolution: 2.9→53.23 Å / Isotropic thermal model: anisotropic / Cross valid method: thoughout / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1089 -random
Rwork0.24 ---
all-24314 --
obs-22661 93.2 %-
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1--9.69 Å20 Å20 Å2
2--25.88 Å20 Å2
3----16.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.9→53.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 3 4 3525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.038
RfactorNum. reflection% reflection
Rfree0.479 161 -
Rwork0.412 --
obs-3193 84.4 %

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