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- PDB-2wyq: THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23... -

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Basic information

Entry
Database: PDB / ID: 2wyq
TitleTHE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)
ComponentsUV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
KeywordsDNA BINDING PROTEIN / DNA EXCISION REPAIR / PROTEASOMAL DEGRADATION / POLYUBIQUITIN
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair ...regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair / DNA Damage Recognition in GG-NER / protein destabilization / kinase binding / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain ...RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsChen, Y.W.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2011
Title: The Crystal Structure of the Ubiquitin-Like (Ubl) Domain of Human Homologue a of Rad23 (Hhr23A) Protein
Authors: Chen, Y.W. / Tajima, T. / Agrawal, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Ubiquitin-Like (Ubl) Domain of the Human Homologue a of Rad23 (Hhr23A) Protein.
Authors: Chen, Y.W. / Tajima, T. / Rees, M. / Garcia-Maya, M.
#2: Journal: Embo J. / Year: 2003
Title: Structural Determinants for the Binding of Ubiquitin-Like Domains to the Proteasome.
Authors: Mueller, T.D. / Feigon, J.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: DNA-Repair Protein Hhr23A Alters its Protein Structure Upon Binding Proteasomal Subunit S5A.
Authors: Walters, K.J. / Lech, P.J. / Goh, A.M. / Wang, Q. / Howley, P.M.
History
DepositionNov 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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_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_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: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7713
Polymers9,5791
Non-polymers1922
Water1,946108
1
A: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
hetero molecules

A: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5436
Polymers19,1592
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1250 Å2
ΔGint-59.9 kcal/mol
Surface area8750 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.434, 78.434, 63.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1079-

SO4

21A-2029-

HOH

31A-2106-

HOH

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Components

#1: Protein UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A / HHR23A


Mass: 9579.271 Da / Num. of mol.: 1 / Fragment: UBIQUITIN-LIKE DOMAIN, RESIDUES 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: P54725
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLONING ARTIFACT GLY ILE PRO.

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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: 3.04 Å3/Da / Density % sol: 59.5 %
Description: THIS IS A COMBINED DATASET, OF 1.65A SYNCHROTRON DATA AND OF 1.97A INHOUSE DATA. THE EXPERIMENTAL DETAILS INCLUDED HERE ARE THOSE USED FOR THE SYNCHROTRON DATASET. THE DATA REDUCTION ...Description: THIS IS A COMBINED DATASET, OF 1.65A SYNCHROTRON DATA AND OF 1.97A INHOUSE DATA. THE EXPERIMENTAL DETAILS INCLUDED HERE ARE THOSE USED FOR THE SYNCHROTRON DATASET. THE DATA REDUCTION STATISTICS ARE THOSE FOR THE COMBINED DATASET.
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→63.57 Å / Num. obs: 14363 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 36.17 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.86
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 23 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.08 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BWF

2bwf


Resolution: 1.651→35 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.999 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 706 4.97 %RANDOM
Rwork0.1241 ---
obs0.126 14330 99.902 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 9.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.026 Å20.013 Å2-0 Å2
2--0.026 Å2-0 Å2
3----0.039 Å2
Refinement stepCycle: LAST / Resolution: 1.651→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 10 108 721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022670
X-RAY DIFFRACTIONr_bond_other_d0.0010.02467
X-RAY DIFFRACTIONr_angle_refined_deg2.2882905
X-RAY DIFFRACTIONr_angle_other_deg3.11331158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.351580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59824.81527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99215141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.156154
X-RAY DIFFRACTIONr_chiral_restr0.2760.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021688
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02120
X-RAY DIFFRACTIONr_nbd_refined0.2990.2115
X-RAY DIFFRACTIONr_nbd_other0.1890.2411
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2292
X-RAY DIFFRACTIONr_nbtor_other0.0950.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5761.5402
X-RAY DIFFRACTIONr_mcbond_other1.1711.5158
X-RAY DIFFRACTIONr_mcangle_it3.5532670
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4233268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.414.5235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.47931137
X-RAY DIFFRACTIONr_sphericity_free20.1265108
X-RAY DIFFRACTIONr_sphericity_bonded5.56651130
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 50 -
Rwork0.097 974 -
obs--98.746 %
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)
121.585-0.2471-1.28364.5680.25373.6019-0.27670.4617-0.8059-0.30790.137-0.76320.54530.59310.13980.19160.016-0.00330.21020.00070.160.519923.3891-1.2905
28.55582.50240.80074.5164-0.48515.4426-0.03030.54140.2774-0.0953-0.02650.2031-0.3064-0.10630.05690.1295-0.0341-0.05810.17560.01460.0789-16.035926.445-0.4474
311.97232.8139-0.58579.34582.25426.05460.09560.6605-0.7727-0.65280.1076-0.5040.69040.1207-0.20330.13810.0061-0.01560.2040.04160.0922-0.950727.0401-3.5507
414.4422-3.4529-0.55467.4521-2.535210.680.08010.23590.3831-0.33830.0712-0.4164-0.10180.7047-0.15120.0946-0.0348-0.0490.19050.03120.07023.401531.40224.7618
54.899-1.11182.79012.7246-2.32810.1088-0.00280.18660.31740.01340.0657-0.1286-0.2020.2383-0.06280.0861-0.029-0.02140.15570.0640.1003-4.761935.43911.2442
612.4497-0.9178-0.598714.0299-2.879713.65380.0841-0.0650.0916-0.03940.05690.3904-0.0841-0.2048-0.1410.0919-0.0284-0.04630.16210.09340.1203-13.127237.4093-1.8452
72.23-0.10470.097315.4271-4.30294.34480.12840.04690.16530.3241-0.01160.0718-0.1311-0.0252-0.11690.0842-0.0297-0.04260.17860.01550.068-10.126331.94458.1802
84.8721.1062-0.93661.8004-0.90072.9205-0.01480.07630.03020.01650.0104-0.03450.1350.07440.00440.10680.0149-0.06660.11410.00180.0617-1.511227.636511.7442
93.48523.99984.61284.66666.176816.33950.0770.4733-0.6841-0.1526-0.2321-0.2950.83340.2640.15510.1611-0.0219-0.02960.1698-0.01450.1388-1.368320.27317.2559
107.549-1.9177-0.601610.92451.67484.9107-0.09480.1001-0.14650.3270.1116-0.0460.3075-0.0749-0.01690.1366-0.0496-0.03490.21450.0430.0606-11.749624.41744.5295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 15
3X-RAY DIFFRACTION3A16 - 19
4X-RAY DIFFRACTION4A20 - 26
5X-RAY DIFFRACTION5A27 - 34
6X-RAY DIFFRACTION6A35 - 41
7X-RAY DIFFRACTION7A42 - 50
8X-RAY DIFFRACTION8A51 - 63
9X-RAY DIFFRACTION9A64 - 68
10X-RAY DIFFRACTION10A69 - 77

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