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- PDB-2clw: Crystal structure of human ubiquitin-conjugating enzyme UbcH5B -

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Basic information

Entry
Database: PDB / ID: 2clw
TitleCrystal structure of human ubiquitin-conjugating enzyme UbcH5B
Components(UBIQUITIN-CONJUGATING ENZYME E2 D2) x 2
KeywordsLIGASE / UBL CONJUGATION PATHWAY / UBC DOMAIN / THIOESTERIFICATION
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / protein modification process / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 Å
AuthorsDodd, R.B. / Read, R.J.
CitationJournal: To be Published
Title: Structures of Two Human Ubiquitin-Conjugating Enzymes from Twinned Crystals
Authors: Dodd, R.B. / Read, R.J.
History
DepositionMay 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
SupersessionAug 13, 2014ID: 2C4O
Revision 1.1Aug 13, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2 D2
B: UBIQUITIN-CONJUGATING ENZYME E2 D2
C: UBIQUITIN-CONJUGATING ENZYME E2 D2
D: UBIQUITIN-CONJUGATING ENZYME E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7598
Polymers75,3874
Non-polymers3724
Water4,864270
1
A: UBIQUITIN-CONJUGATING ENZYME E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1844
Polymers18,9041
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UBIQUITIN-CONJUGATING ENZYME E2 D2


Theoretical massNumber of molelcules
Total (without water)18,8281
Polymers18,8281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UBIQUITIN-CONJUGATING ENZYME E2 D2


Theoretical massNumber of molelcules
Total (without water)18,8281
Polymers18,8281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UBIQUITIN-CONJUGATING ENZYME E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9202
Polymers18,8281
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.585, 65.803, 101.677
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99982, 0.00724, -0.01767), (-0.00676, -0.99961, -0.02725), (-0.01786, -0.02713, 0.99947)22.33517, 27.01925, -24.26884
2given(0.99609, 0.00287, 0.0883), (-0.00404, 0.99991, 0.01307), (-0.08825, -0.01337, 0.99601)-3.9232, -0.24234, -50.41184
3given(0.99273, -0.02848, -0.11698), (-0.03281, -0.99884, -0.03525), (-0.11584, 0.03883, -0.99251)-18.54609, -4.85658, 28.47761

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBCH5B / UBIQUITIN-PROTEIN LIGASE D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME ...UBCH5B / UBIQUITIN-PROTEIN LIGASE D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / E2(17)KB 2


Mass: 18903.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUE A 85 HAS BEEN MODIFIED FROM CYSTEINE BY 2-MERCAPTOETHANOL TO FORM S, S-(2-HYDROXYETHYL) THIOCYSTEINE
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-12 (EMBL) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBCH5B / UBIQUITIN-PROTEIN LIGASE D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME ...UBCH5B / UBIQUITIN-PROTEIN LIGASE D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / E2(17)KB 2


Mass: 18827.666 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-12 (EMBL) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P62837, ubiquitin-protein ligase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESPONSIBLE FOR THE UBIQUITINATION OF OTHER PROTEINS. IT ALSO TAKES PART IN THE DEGRADATION OF ...RESPONSIBLE FOR THE UBIQUITINATION OF OTHER PROTEINS. IT ALSO TAKES PART IN THE DEGRADATION OF ABNORMAL AND SHORT-LIVED PROTEINS.
Has protein modificationY
Sequence detailsIN ADDITION TO THE RGS SEQUENCE PRECEDING THE UNIPROT UBCH5B SEQUENCE, THE FOLLOWING RESIDUES WERE ...IN ADDITION TO THE RGS SEQUENCE PRECEDING THE UNIPROT UBCH5B SEQUENCE, THE FOLLOWING RESIDUES WERE PRESENT IN THE STRUCTURE, BUT NOT LOCATED IN THE ELECTRON DENSITY MAPS,PRESUMABLY DUE TO DISORDER: MKHHHHHHPMSGLVP

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.06 %
Crystal growpH: 4.6
Details: 150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9821
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9821 Å / Relative weight: 1
ReflectionResolution: 1.94→30.23 Å / Num. obs: 602165 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.36 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.43
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.53 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QCQ

1qcq


Resolution: 1.945→30.124 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1418061.63 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ
Details: DUE TO THE PRESENCE OF ORTHORHOMBIC PSEUDOSYMMETRY, THE TEST SET OF REFLECTIONS WERE CHOSEN IN P212121 AND THEN EXPANDED TO COVER THE MONOCLINIC SPACE GROUP. DATA WERE FOUND TO BE NEAR- ...Details: DUE TO THE PRESENCE OF ORTHORHOMBIC PSEUDOSYMMETRY, THE TEST SET OF REFLECTIONS WERE CHOSEN IN P212121 AND THEN EXPANDED TO COVER THE MONOCLINIC SPACE GROUP. DATA WERE FOUND TO BE NEAR- PERFECTLY TWINNED AND WERE THEREFORE TREATED AS PERFECTLY TWINNED. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT WITH POSITIONAL RESTRAINTS OF 30 KCAL/MOL-A**2 (300 INITIALLY) AND B-FACTOR TARGET SIGMA OF 2.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1116 2.5 %RANDOM
Rwork0.218 ---
obs0.218 44131 99.5 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL / Bsol: 77.0658 Å2 / ksol: 0.371453 e/Å3
Displacement parametersBiso mean: 32.38 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20 Å2
2--1.069 Å20 Å2
3----3.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 1.945→30.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 23 270 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 1.94→2.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.312 116 2.2 %
Rwork0.302 5223 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_CME.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CME.PARCME.TOP
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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