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- PDB-2a7l: Structure of the human hypothetical ubiquitin-conjugating enzyme,... -

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Basic information

Entry
Database: PDB / ID: 2a7l
TitleStructure of the human hypothetical ubiquitin-conjugating enzyme, LOC55284
ComponentsHypothetical ubiquitin-conjugating enzyme LOC55284
KeywordsLIGASE / STRUCTURAL GENOMICS CONSORTIUM / (SGC) / UBIQUITIN / UBIQUITIN- CONJUGATING ENZYME
Function / homology
Function and homology information


N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of TORC1 signaling / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of TORC1 signaling / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 W
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Aug 23, 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 / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical ubiquitin-conjugating enzyme LOC55284
B: Hypothetical ubiquitin-conjugating enzyme LOC55284
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3654
Polymers30,3192
Non-polymers462
Water3,603200
1
A: Hypothetical ubiquitin-conjugating enzyme LOC55284
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1822
Polymers15,1591
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical ubiquitin-conjugating enzyme LOC55284
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1822
Polymers15,1591
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.595, 60.655, 133.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a monomer.

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Components

#1: Protein Hypothetical ubiquitin-conjugating enzyme LOC55284


Mass: 15159.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ11011 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96B02, ubiquitin-protein ligase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.63 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3 M NaCl, 0.1 M bisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 27952 / Num. obs: 27952 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.68
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.94 / Num. unique all: 1475 / % possible all: 50.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y6L

1y6l


Resolution: 1.82→24.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.446 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29982 1403 5 %RANDOM
Rwork0.26179 ---
obs0.26378 26406 95.15 %-
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 mean: 36.259 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å20 Å2
2--4.09 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.82→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 2 200 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221970
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9752676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17125.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.118156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021472
X-RAY DIFFRACTIONr_nbd_refined0.220.2850
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.235
X-RAY DIFFRACTIONr_mcbond_it1.69531234
X-RAY DIFFRACTIONr_mcangle_it2.77442012
X-RAY DIFFRACTIONr_scbond_it3.7055762
X-RAY DIFFRACTIONr_scangle_it5.6457664
LS refinement shellResolution: 1.82→1.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.521 69 -
Rwork0.454 1241 -
obs--61.91 %

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