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- PDB-3m63: Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL... -

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Basic information

Entry
Database: PDB / ID: 3m63
TitleCrystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2
Components
  • Ubiquitin conjugation factor E4
  • Ubiquitin domain-containing protein DSK2
KeywordsLIGASE/PROTEIN BINDING / Armadillo-like repeats / Ubl conjugation pathway / Nucleus / Phosphoprotein / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / K48-linked polyubiquitin modification-dependent protein binding / ubiquitin-ubiquitin ligase activity / cellular response to ethanol / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / ubiquitin ligase complex / protein K48-linked ubiquitination ...Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / K48-linked polyubiquitin modification-dependent protein binding / ubiquitin-ubiquitin ligase activity / cellular response to ethanol / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / ubiquitin ligase complex / protein K48-linked ubiquitination / ERAD pathway / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / protein ubiquitination / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain ...Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / U-box domain / U-box domain profile. / Modified RING finger domain / U-box 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 domain signature. / Ubiquitin conserved site / 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
: / Ubiquitin domain-containing protein DSK2 / 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _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.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.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_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: Ubiquitin domain-containing protein DSK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,3462
Non-polymers2772
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.130, 125.700, 181.210
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 Ubiquitin domain-containing protein DSK2


Mass: 11539.952 Da / Num. of mol.: 1 / Fragment: UNP residues 1-75, Ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DSK2, SHE4, YM8021.02, YMR276W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: P48510
#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.: 183 / 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: 59.42 %
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: ESRF / Beamline: ID14-4 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→73.501 Å / Num. all: 58089 / Num. obs: 58089 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.2 / Num. unique all: 58089 / Rsym value: 0.509 / % possible all: 95.1

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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→73.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 19.187 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.321 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2951 5.1 %RANDOM
Rwork0.206 ---
all0.21 58038 --
obs0.21 58038 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 110.92 Å2 / Biso mean: 42.881 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→73.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8269 0 17 183 8469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228476
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9711450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27751022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29324.758414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.834151534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8441544
X-RAY DIFFRACTIONr_chiral_restr0.1120.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216377
X-RAY DIFFRACTIONr_mcbond_it1.1325134
X-RAY DIFFRACTIONr_mcangle_it2.11338336
X-RAY DIFFRACTIONr_scbond_it3.3564.53342
X-RAY DIFFRACTIONr_scangle_it5.01663113
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 181 -
Rwork0.289 3698 -
all-3879 -
obs--90.46 %
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)
10.657-0.081-0.04831.627-0.46081.80060.10260.2046-0.0898-0.627-0.1519-0.21220.25330.09370.04930.44820.12270.07130.18280.00810.132643.0292-22.5259-53.2683
20.4104-0.5593-0.2651.43370.3740.62170.1190.1012-0.0125-0.0733-0.02820.1644-0.1815-0.1225-0.09080.18460.04260.04280.16480.05250.137324.971-12.0726-20.8211
31.6753-0.1191-0.71771.3465-0.66462.87140.0781-0.1435-0.1443-0.1465-0.028-0.06020.12670.1006-0.050.1244-0.04170.00830.1508-0.01160.105322.2492-12.949912.15
44.3839-1.18674.24272.8142-2.08211.3138-0.0262-0.5701-0.4197-0.03340.18450.2838-0.1896-1.4956-0.15820.08110.05620.00590.37040.00970.1267-10.4041-2.913826.9552
58.5915-7.21792.98068.1862-2.48031.06530.02841.5856-0.2299-1.53210.0515-0.019-0.1540.4309-0.07991.859-0.2922-0.02951.8101-0.29590.187232.4158-25.1524-82.2511
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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