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- PDB-3m62: Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL... -

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Basic information

Entry
Database: PDB / ID: 3m62
TitleCrystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23
Components
  • UV excision repair protein RAD23
  • Ubiquitin conjugation factor E4
KeywordsLIGASE/PROTEIN BINDING / Armadillo-like repeats / Ubl conjugation pathway / DNA damage / DNA repair / Nucleus / Phosphoprotein / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


PNGase complex / nucleotide-excision repair factor 2 complex / ubiquitin-dependent glycoprotein ERAD pathway / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / ubiquitin-ubiquitin ligase activity / proteasome binding / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / protein K48-linked ubiquitination ...PNGase complex / nucleotide-excision repair factor 2 complex / ubiquitin-dependent glycoprotein ERAD pathway / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / ubiquitin-ubiquitin ligase activity / proteasome binding / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / protein K48-linked ubiquitination / ERAD pathway / ubiquitin ligase complex / ubiquitin binding / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein polyubiquitination / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / protein ubiquitination / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin conjugation factor E4 / Ubiquitin conjugation factor E4, core / Ubiquitin elongating factor core / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / U-box domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. ...Ubiquitin conjugation factor E4 / Ubiquitin conjugation factor E4, core / Ubiquitin elongating factor core / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / U-box domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / U-box domain profile. / Modified RING finger domain / U-box domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / UV excision repair protein RAD23 / E4 ubiquitin-protein ligase UFD2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain.
Authors: Hanzelmann, P. / Stingele, J. / Hofmann, K. / Schindelin, H. / Raasi, S.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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 conjugation factor E4
B: UV excision repair protein RAD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9694
Polymers122,6922
Non-polymers2772
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.040, 126.550, 180.870
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 conjugation factor E4 / Ubiquitin fusion degradation protein 2 / UB fusion protein 2


Mass: 110806.328 Da / Num. of mol.: 1 / Mutation: S102L, D677V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D1255, UFD2, YDL190C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: P54860
#2: Protein UV excision repair protein RAD23


Mass: 11885.586 Da / Num. of mol.: 1 / Fragment: UNP residues 1-84, Ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD23, SYGP-ORF29, YEL037C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: P32628
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 18, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→45.22 Å / Num. all: 59314 / Num. obs: 59314 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.3 / Num. unique all: 59314 / Rsym value: 0.492 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QIZ

2qiz


Resolution: 2.4→45.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.58 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.307 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2973 5 %RANDOM
Rwork0.2 ---
all0.203 59241 --
obs0.203 59241 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.67 Å2 / Biso mean: 25.733 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---0.08 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 17 298 8587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228485
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.97511456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51951023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94224.816407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.559151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2081543
X-RAY DIFFRACTIONr_chiral_restr0.1180.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216344
X-RAY DIFFRACTIONr_mcbond_it1.1225147
X-RAY DIFFRACTIONr_mcangle_it2.04838369
X-RAY DIFFRACTIONr_scbond_it3.3934.53338
X-RAY DIFFRACTIONr_scangle_it4.90563087
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 203 -
Rwork0.234 4087 -
all-4290 -
obs--100 %
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)
10.6068-0.0953-0.24771.5852-0.64863.02360.05950.2074-0.1376-0.5912-0.214-0.21650.35190.1570.15450.27330.1170.06160.1240.0090.175143.0491-22.5573-53.211
20.4501-0.7426-0.22443.30320.53460.78110.05860.0595-0.0322-0.0231-0.00750.3837-0.2265-0.1915-0.05110.08430.02940.04540.17240.03780.135324.9504-12.3169-20.8725
31.71550.0472-0.43143.0384-0.82943.44460.0275-0.0837-0.2788-0.1692-0.0078-0.07560.30940.0356-0.01970.039-0.02180.00390.1444-0.01160.100722.1517-13.1312.0491
44.6673-0.83673.61043.4966-1.40828.8365-0.0706-0.6794-0.43460.2150.14570.2381-0.1401-1.0529-0.07520.03210.06440.01780.28080.02220.1854-10.4431-3.035926.6116
58.16-1.36320.79975.1992-0.6326.5487-0.29040.7206-0.5682-1.15640.1840.34730.4268-0.62390.10640.9186-0.0705-0.00750.55-0.08660.308331.6859-24.0576-82.1129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 326
2X-RAY DIFFRACTION2A327 - 610
3X-RAY DIFFRACTION3A611 - 872
4X-RAY DIFFRACTION4A873 - 953
5X-RAY DIFFRACTION5B1 - 72

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