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- PDB-6w2h: Crystal Structure of the Internal UBA Domain of HHR23A -

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Basic information

Entry
Database: PDB / ID: 6w2h
TitleCrystal Structure of the Internal UBA Domain of HHR23A
ComponentsUV excision repair protein RAD23 homolog A
KeywordsDNA BINDING PROTEIN / Ubiquitin Associated Domain / UBA Domain / Helical Bundle
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 / protein destabilization / DNA Damage Recognition in GG-NER / 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 / cytosol / cytoplasm
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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
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: 1.6 Å
AuthorsBowler, B.E. / Zeng, B. / Becht, D.C. / Rothfuss, M. / Sprang, S.R. / Mou, T.-C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1412164 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: Biochemistry / Year: 2022
Title: Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A.
Authors: Becht, D.C. / Leavens, M.J. / Zeng, B. / Rothfuss, M.T. / Briknarova, K. / Bowler, B.E.
History
DepositionMar 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 25, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: UV excision repair protein RAD23 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7362
Polymers5,6401
Non-polymers961
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.119, 31.119, 40.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein UV excision repair protein RAD23 homolog A / hHR23A


Mass: 5640.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Plasmid: pGEX-2T
Details (production host): Thrombin cleavage site replaced with TEV protease cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54725
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.74 Å3/Da / Density % sol: 29.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH 8.5, 1.5 M Ammonium sulfate, 12%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→31.12 Å / Num. obs: 5180 / % possible obs: 99.71 % / Redundancy: 13.2 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0876 / Rpim(I) all: 0.02491 / Rrim(I) all: 0.09114 / Net I/σ(I): 21.45
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.8064 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 534 / CC1/2: 0.926 / CC star: 0.98 / Rpim(I) all: 0.2341 / Rrim(I) all: 0.8403 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER1.17.1-3660phasing
PHENIX1.17.1-3660model building
Coot0.8.9.2 ELmodel building
PHENIX1.17.1-3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P43 UBA-1 Y188G Structure Solved by Sulfur SAD

Resolution: 1.6→31.12 Å / SU ML: 0.1316 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.2717
RfactorNum. reflection% reflection
Rfree0.2054 517 10 %
Rwork0.1618 --
obs0.1662 5168 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms384 0 5 43 432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046403
X-RAY DIFFRACTIONf_angle_d0.7048548
X-RAY DIFFRACTIONf_chiral_restr0.049862
X-RAY DIFFRACTIONf_plane_restr0.004270
X-RAY DIFFRACTIONf_dihedral_angle_d5.878660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.760.23321320.18261171X-RAY DIFFRACTION99.54
1.76-2.020.24071240.16371147X-RAY DIFFRACTION99.84
2.02-2.540.20461300.16021155X-RAY DIFFRACTION99.84
2.54-31.120.19021310.15761178X-RAY DIFFRACTION99.7

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