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- PDB-6op8: S. pombe Ubc7/U7BR complex -

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Basic information

Entry
Database: PDB / ID: 6op8
TitleS. pombe Ubc7/U7BR complex
Components
  • CUE domain-containing protein 4, mitochondrial
  • Ubiquitin-conjugating enzyme E2-18 kDa
KeywordsLIGASE/PROTEIN BINDING / UBL CONJUGATION PATHWAY / ENDOPLASMIC RETICULUM-ASSOCIATED DEGRADATION / LIGASE / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


inner nuclear membrane-associated protein degradation pathway / Hrd1p ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-protein transferase activator activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ERAD pathway / ubiquitin binding / protein ubiquitination ...inner nuclear membrane-associated protein degradation pathway / Hrd1p ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-protein transferase activator activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ERAD pathway / ubiquitin binding / protein ubiquitination / endoplasmic reticulum / mitochondrion / ATP binding / nucleus / cytosol
Similarity search - Function
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 ...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 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2-18 kDa / CUE domain-containing protein 4, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsHann, Z.S. / Lima, C.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118080 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the Schizosaccharomyces pombe U7BR E2-binding region in complex with Ubc7.
Authors: Hann, Z.S. / Metzger, M.B. / Weissman, A.M. / Lima, C.D.
History
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2-18 kDa
B: CUE domain-containing protein 4, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1315
Polymers27,0222
Non-polymers1093
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.715, 79.047, 94.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 19206.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: ubc7, ubcp3, SPBP16F5.04 / Plasmid: pET29b / Production host: Escherichia coli (E. coli)
References: UniProt: O00102, E2 ubiquitin-conjugating enzyme
#2: Protein CUE domain-containing protein 4, mitochondrial


Mass: 7814.836 Da / Num. of mol.: 1 / Fragment: residues 152-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: SPCC4G3.13c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P87238

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Non-polymers , 4 types, 217 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.85 Å3/Da / Density % sol: 33.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM TRIS, pH 8.0, 200 mM MgCl2, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.703→47.2787 Å / Num. obs: 22673 / % possible obs: 99.39 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0562 / Rpim(I) all: 0.02523 / Rrim(I) all: 0.06177 / Net I/σ(I): 25.94
Reflection shellResolution: 1.703→1.764 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.2232 / Mean I/σ(I) obs: 9.05 / Num. unique obs: 2195 / CC1/2: 0.97 / Rpim(I) all: 0.1023 / Rrim(I) all: 0.2461 / % possible all: 98.12

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQU

4jqu


Resolution: 1.703→47.26 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.188 1170 5.17 %
Rwork0.1549 --
obs0.1567 22635 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.47 Å2 / Biso mean: 20.4469 Å2 / Biso min: 3.7 Å2
Refinement stepCycle: final / Resolution: 1.703→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 6 214 1896
Biso mean--34.27 27.88 -
Num. residues----210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7029-1.78040.23391290.17792625275498
1.7804-1.87430.21281370.16792609274699
1.8743-1.99170.23421340.165126402774100
1.9917-2.14550.17121470.151326582805100
2.1455-2.36140.16991600.139626602820100
2.3614-2.70310.1951630.149426852848100
2.7031-3.40550.19131620.156927112873100
3.4055-47.27870.1731380.15462877301599

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