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- PDB-4jqu: Crystal structure of Ubc7p in complex with the U7BR of Cue1p -

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Basic information

Entry
Database: PDB / ID: 4jqu
TitleCrystal structure of Ubc7p in complex with the U7BR of Cue1p
Components
  • Coupling of ubiquitin conjugation to ER degradation protein 1
  • Ubiquitin-conjugating enzyme E2 7
KeywordsLIGASE/PROTEIN BINDING / Ubc7p:U7BR complex / ligase-activator complex / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


CUE1-UBC7 ubiquitin-conjugating enzyme complex / establishment of protein localization to endoplasmic reticulum membrane / Doa10p ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / ubiquitin-protein transferase activator activity / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / : ...CUE1-UBC7 ubiquitin-conjugating enzyme complex / establishment of protein localization to endoplasmic reticulum membrane / Doa10p ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / ubiquitin-protein transferase activator activity / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / : / ERAD pathway / ubiquitin conjugating enzyme activity / response to cadmium ion / ubiquitin binding / ubiquitin-protein transferase activity / chromatin organization / ubiquitin-dependent protein catabolic process / protein ubiquitination / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / ATP binding / cytosol
Similarity search - Function
Helix Hairpins - #4310 / Cue1, Ubc7p-binding domain / Ubc7p-binding region of Cue1 / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site ...Helix Hairpins - #4310 / Cue1, Ubc7p-binding domain / Ubc7p-binding region of Cue1 / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Coupling of ubiquitin conjugation to ER degradation protein 1 / Ubiquitin-conjugating enzyme E2 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsLiang, Y.-H. / Metzger, M.B. / Weissman, A.M. / Ji, X.
CitationJournal: Mol.Cell / Year: 2013
Title: A Structurally Unique E2-Binding Domain Activates Ubiquitination by the ERAD E2, Ubc7p, through Multiple Mechanisms.
Authors: Metzger, M.B. / Liang, Y.H. / Das, R. / Mariano, J. / Li, S. / Li, J. / Kostova, Z. / Byrd, R.A. / Ji, X. / Weissman, A.M.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.4Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 7
B: Coupling of ubiquitin conjugation to ER degradation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6715
Polymers25,2502
Non-polymers4213
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-10 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.810, 48.463, 95.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 7 / Ubc7p / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2-18 kDa / Ubiquitin-protein ligase


Mass: 18764.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: QRI8, UBC7, Ubc7p, YM9711.12, YMR022W / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(star) / References: UniProt: Q02159, ubiquitin-protein ligase
#2: Protein Coupling of ubiquitin conjugation to ER degradation protein 1 / Cue1p / Kinetochore-defect suppressor 4


Mass: 6485.444 Da / Num. of mol.: 1 / Fragment: U7BR (UNP residues 151-203)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CUE1, Cue1p, KIS4, YM8156.06, YMR264W / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(star) / References: UniProt: P38428
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2009
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→40 Å / Num. all: 20415 / Num. obs: 20415 / % possible obs: 98.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.008 / Net I/σ(I): 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.81-1.876.40.4943.418990.97493.7
1.87-1.957.30.3815.219731.01197.4
1.95-2.047.40.259820081.01498.4
2.04-2.157.50.17312.119871.02898.8
2.15-2.287.50.12616.320301.0499.5
2.28-2.467.60.09420.920511.00899.5
2.46-2.77.80.07725.820620.99799.9
2.7-3.0980.07227.320791.044100
3.09-3.980.05928.220981.008100
3.9-407.50.03539.222280.95599.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UCZ

2ucz


Resolution: 1.81→33.467 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.854 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 905 4.47 %RANDOM
Rwork0.1845 ---
obs0.1863 20262 98.77 %-
all-20262 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.188 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 29.9678 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1-4.277 Å2-0 Å2-0 Å2
2---2.7651 Å20 Å2
3----1.5118 Å2
Refinement stepCycle: LAST / Resolution: 1.81→33.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 28 136 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051905
X-RAY DIFFRACTIONf_angle_d0.9742597
X-RAY DIFFRACTIONf_chiral_restr0.063288
X-RAY DIFFRACTIONf_plane_restr0.005342
X-RAY DIFFRACTIONf_dihedral_angle_d17.162759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.81-1.92340.24851430.213730743217321796
1.9234-2.07190.24481470.190631453292329298
2.0719-2.28040.24971500.185131973347334799
2.2804-2.61020.23281520.1879324133933393100
2.6102-3.28820.22691570.1933326834253425100
3.2882-33.47280.20331560.171343235883588100

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