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- PDB-6nyd: Crystal Structure of S. cerevisiae Ubc3 (Cdc34) -

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Basic information

Entry
Database: PDB / ID: 6nyd
TitleCrystal Structure of S. cerevisiae Ubc3 (Cdc34)
ComponentsUbiquitin-conjugating enzyme E2-34 kDa
KeywordsLIGASE/TRANSFERASE / CONFORMATIONAL CHANGE / THIOESTER / ADENYLATION / THIOESTER TRANSFER / TRANSTHIOESTERIFICATION / ATP-BINDING / UBIQUITIN E2-BINDING / UBIQUITINATION / LIGASE / LIGASE-TRANSFERASE complex
Function / homology
Function and homology information


regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / regulation of metabolic process / positive regulation of glucose transmembrane transport / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme ...regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / regulation of metabolic process / positive regulation of glucose transmembrane transport / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / SCF ubiquitin ligase complex / ubiquitin conjugating enzyme activity / regulation of mitotic cell cycle / subtelomeric heterochromatin formation / protein autoubiquitination / G1/S transition of mitotic cell cycle / protein polyubiquitination / ubiquitin-protein transferase activity / G2/M transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA replication / chromosome, telomeric region / cell division / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ubiquitin-conjugating enzyme E2-34 kDa
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsOlsen, S.K. / Williams, K.M. / Atkison, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115568 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34.
Authors: Williams, K.M. / Qie, S. / Atkison, J.H. / Salazar-Arango, S. / Alan Diehl, J. / Olsen, S.K.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin-conjugating enzyme E2-34 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8668
Polymers22,4271
Non-polymers4397
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.084, 49.022, 103.684
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 E2-34 kDa / Cell division control protein 34 / E2 ubiquitin-conjugating enzyme 3 / E3 ubiquitin ligase complex ...Cell division control protein 34 / E2 ubiquitin-conjugating enzyme 3 / E3 ubiquitin ligase complex SCF subunit CDC34 / Ubiquitin carrier protein / Ubiquitin-protein ligase


Mass: 22427.152 Da / Num. of mol.: 1 / Fragment: residues 3-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C / Plasmid: PET29NTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) codon plus
References: UniProt: P14682, E2 ubiquitin-conjugating enzyme
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.06 M zinc acetate, 0.108mM sodium cacodylate, 14.4% PEG 8,000, 20% glycerol

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Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 28, 2016
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 25422 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Net I/σ(I): 20
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 1.151 / CC1/2: 0.609 / Rpim(I) all: 0.511

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDK

4mdk


Resolution: 1.65→37.387 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.37
RfactorNum. reflection% reflection
Rfree0.1991 1999 7.88 %
Rwork0.1708 --
obs0.1731 25353 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→37.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 16 103 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011450
X-RAY DIFFRACTIONf_angle_d1.0721978
X-RAY DIFFRACTIONf_dihedral_angle_d13.221901
X-RAY DIFFRACTIONf_chiral_restr0.059212
X-RAY DIFFRACTIONf_plane_restr0.008264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.648-1.68920.33151400.29061640X-RAY DIFFRACTION99
1.6892-1.73490.25971410.24841638X-RAY DIFFRACTION100
1.7349-1.78590.27141400.22121634X-RAY DIFFRACTION100
1.7859-1.84360.25381410.21141647X-RAY DIFFRACTION100
1.8436-1.90940.21961420.19971660X-RAY DIFFRACTION100
1.9094-1.98590.21111410.18081644X-RAY DIFFRACTION100
1.9859-2.07630.21461410.17281646X-RAY DIFFRACTION100
2.0763-2.18570.1851420.16251674X-RAY DIFFRACTION100
2.1857-2.32260.18691420.15681652X-RAY DIFFRACTION100
2.3226-2.50190.19581430.16131679X-RAY DIFFRACTION100
2.5019-2.75360.20391440.16661674X-RAY DIFFRACTION100
2.7536-3.15190.19771450.17091692X-RAY DIFFRACTION100
3.1519-3.97040.18241470.15471720X-RAY DIFFRACTION100
3.9704-37.39690.19721500.17311754X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8802-2.1779-1.70776.73812.91353.9576-0.0442-0.2036-0.42720.0136-0.28330.21890.6059-0.3050.16040.2091-0.0183-0.0160.31760.04570.238811.4364-15.0201-1.0817
25.29870.07872.47272.11932.24085.3770.33040.2238-0.42990.02910.1197-0.59660.53720.4758-0.20230.40810.0611-0.02730.4863-0.03810.463216.7942-18.2288-12.5315
33.2710.89931.1942.21990.2997.05620.03150.3082-0.1962-0.22690.1235-0.28120.6346-0.0399-0.13990.2823-0.03080.02920.24960.00960.296611.5655-15.0377-21.7969
44.355-1.4827-1.46122.03371.02043.08430.1662-0.50380.22090.10450.1217-0.1365-0.55170.0911-0.11680.2065-0.013-0.02140.26180.01470.29247.9573-7.175-8.429
53.71620.1701-0.36271.3952-2.4246.61160.20290.24960.51270.1235-0.0374-0.4756-1.01340.23980.03570.30430.02820.02590.23750.04770.36449.4645-4.33-22.0443
64.4068-2.27810.95191.23520.13797.6004-0.1670.00920.57-0.10150.1792-0.0105-0.583-0.589-0.13940.33480.0181-0.02590.22060.02120.35752.7263-3.0104-21.0386
79.5614-5.10233.60676.7732-5.09254.07450.00250.90660.46730.02410.07920.4744-0.4622-0.52-0.15650.26020.0340.02030.38570.03560.3541-3.0258-9.8348-8.0642
82.1439-1.24342.56682.9819-3.40696.8617-0.00490.03630.0913-0.3737-0.04680.02390.0816-0.0681-0.14970.31740.0139-0.03140.1944-0.00310.2756-1.1175-8.6704-26.5384
93.9172-3.4954.76464.7569-2.51278.40550.13651.17940.3067-1.3257-0.4231-0.78180.18450.92180.21610.5456-0.03380.10140.42190.00810.384611.13-8.9479-35.2112
106.6348-5.2171-2.04764.5773-0.02866.4177-0.85150.6692-0.50170.70670.306-1.13210.4190.00440.24740.55110.12020.05050.7525-0.17930.922322.153-19.3868-24.0609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 3 through 20 )
2X-RAY DIFFRACTION2chain 'C' and (resid 21 through 37 )
3X-RAY DIFFRACTION3chain 'C' and (resid 38 through 59 )
4X-RAY DIFFRACTION4chain 'C' and (resid 60 through 75 )
5X-RAY DIFFRACTION5chain 'C' and (resid 76 through 84 )
6X-RAY DIFFRACTION6chain 'C' and (resid 85 through 99 )
7X-RAY DIFFRACTION7chain 'C' and (resid 100 through 120 )
8X-RAY DIFFRACTION8chain 'C' and (resid 121 through 152 )
9X-RAY DIFFRACTION9chain 'C' and (resid 153 through 170 )
10X-RAY DIFFRACTION10chain 'C' and (resid 171 through 178 )

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