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- PDB-3f92: Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Hunti... -

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Basic information

Entry
Database: PDB / ID: 3f92
TitleCrystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington Interacting Protein 2) M172A mutant crystallized at pH 8.5
ComponentsUbiquitin-conjugating enzyme E2 K
KeywordsLIGASE / Ubiquitin-Conjugating / Huntington Interacting / E2-25K / Ubiquitin-conjugating enzyme E2 K / E2(25K) / Ubiquitin-protein ligase / Ubiquitin carrier protein / Huntington-interacting protein 2 / HIP-2 / Alternative splicing / Cytoplasm / Ubl conjugation / Ubl conjugation pathway
Function / homology
Function and homology information


free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein K48-linked ubiquitination ...free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of peptidyl-threonine phosphorylation / Negative regulators of DDX58/IFIH1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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 / Helicase, Ruva Protein; domain 3 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsWilson, R.C. / Hughes, R.C. / Flatt, J.W. / Meehan, E.J. / Ng, J.D. / Twigg, P.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of full-length ubiquitin-conjugating enzyme E2-25K (huntingtin-interacting protein 2).
Authors: Wilson, R.C. / Hughes, R.C. / Flatt, J.W. / Meehan, E.J. / Ng, J.D. / Twigg, P.D.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8356
Polymers28,2061
Non-polymers6295
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.817, 134.817, 38.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ubiquitin-conjugating enzyme E2 K / E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier ...E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin-conjugating enzyme E2-25K / Ubiquitin-protein ligase


Mass: 28205.840 Da / Num. of mol.: 1 / Mutation: M172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2K, HIP2, LIG / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P61086, E2 ubiquitin-conjugating enzyme

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Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Calcium acetate, Bicine, Tris-HCl, NaCl, PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 16794 / % possible obs: 98.2 % / Observed criterion σ(I): 2.39 / Redundancy: 2.9 % / Biso Wilson estimate: 34.057 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Χ2: 1.272 / Net I/σ(I): 16.01
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.23-2.311.90.37714941.29788.8
2.31-2.42.50.31516221.05296
2.4-2.512.90.24416921.11199.2
2.51-2.643.10.19616961.093100
2.64-2.813.10.14316791.17199.9
2.81-3.033.10.10117051.393100
3.03-3.333.10.07116951.42100
3.33-3.813.10.05517271.42499.8
3.81-4.83.10.04917321.3899.9
4.8-5030.03617521.28998.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.57 Å42.63 Å
Translation2.57 Å42.63 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E46

3e46


Resolution: 2.23→42.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.858 / SU B: 4.35 / SU ML: 0.111 / SU R Cruickshank DPI: 0.172 / SU Rfree: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 852 5.1 %RANDOM
Rwork0.172 ---
obs0.174 15939 98.19 %-
all-16791 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.39 Å2 / Biso mean: 34.513 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.23→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 34 89 1722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221668
X-RAY DIFFRACTIONr_bond_other_d0.0010.021141
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9782270
X-RAY DIFFRACTIONr_angle_other_deg1.07832809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44525.21171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0815282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.739158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_nbd_refined0.2240.2352
X-RAY DIFFRACTIONr_nbd_other0.2060.21099
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2797
X-RAY DIFFRACTIONr_nbtor_other0.0920.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.296
X-RAY DIFFRACTIONr_metal_ion_refined0.1860.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.28
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0750.21
X-RAY DIFFRACTIONr_mcbond_it1.5091.51093
X-RAY DIFFRACTIONr_mcbond_other0.3351.5402
X-RAY DIFFRACTIONr_mcangle_it2.27821684
X-RAY DIFFRACTIONr_scbond_it3.2973693
X-RAY DIFFRACTIONr_scangle_it5.1744.5580
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 49 -
Rwork0.245 1045 -
all-1094 -
obs--87.1 %

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