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- PDB-3e46: Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Hunti... -

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Basic information

Entry
Database: PDB / ID: 3.0E+46
TitleCrystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington interacting protein 2) M172A mutant
ComponentsUbiquitin-conjugating enzyme E2-25 kDa
KeywordsLIGASE / Ubiquitin-Conjugating / Huntington Interacting / E2-25K / 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
Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsHughes, R.C. / Wilson, 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
DepositionAug 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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 1.3Aug 30, 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-conjugating enzyme E2-25 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2462
Polymers28,2061
Non-polymers401
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.490, 134.490, 38.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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


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, ubiquitin-protein ligase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 6
Details: Calcium acetate, Sodium acetate, NaCl, PEG 8000, pH 6.0, 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: Jul 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Number: 109190 / Rmerge(I) obs: 0.081 / Χ2: 1.35 / D res high: 1.84 Å / D res low: 50 Å / Num. obs: 27414 / % possible obs: 90.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.965099.910.0451.2725
3.153.9610010.0731.6295.2
2.753.1510010.1131.3935.2
2.52.7510010.1761.5674.9
2.322.510010.2241.2714.4
2.182.3210010.261.2153.8
2.072.1899.610.2791.0873.1
1.982.0794.310.3331.012.5
1.911.9877.910.410.9931.9
1.841.9131.410.3811.0321.4
ReflectionResolution: 1.86→50 Å / Num. obs: 27414 / % possible obs: 93.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.081
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.98 / Num. unique all: 1674 / Rsym value: 0.374 / % possible all: 52.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.13 Å42.53 Å
Translation2.13 Å42.53 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BEP

2bep


Resolution: 1.86→32.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.846 / SU B: 2.829 / SU ML: 0.081 / SU R Cruickshank DPI: 0.103 / SU Rfree: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1403 5.1 %RANDOM
Rwork0.172 ---
obs0.174 27404 93.87 %-
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: 269.48 Å2 / Biso mean: 36.498 Å2 / Biso min: 17.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.86→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1597 0 1 207 1805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221631
X-RAY DIFFRACTIONr_bond_other_d0.0010.021084
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9622233
X-RAY DIFFRACTIONr_angle_other_deg0.93932673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90625.27872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94515273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.114158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
X-RAY DIFFRACTIONr_nbd_refined0.2330.2379
X-RAY DIFFRACTIONr_nbd_other0.2010.21158
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2831
X-RAY DIFFRACTIONr_nbtor_other0.090.2799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2158
X-RAY DIFFRACTIONr_metal_ion_refined0.2580.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.219
X-RAY DIFFRACTIONr_mcbond_it1.3611.51068
X-RAY DIFFRACTIONr_mcbond_other0.2521.5402
X-RAY DIFFRACTIONr_mcangle_it2.09921676
X-RAY DIFFRACTIONr_scbond_it3.2533662
X-RAY DIFFRACTIONr_scangle_it5.2994.5552
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 55 -
Rwork0.305 1066 -
all-1121 -
obs--52.51 %

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