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- PDB-6w2i: Crystal Structure of Y188G Variant of the Internal UBA Domain of ... -

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Basic information

Entry
Database: PDB / ID: 6w2i
TitleCrystal Structure of Y188G Variant 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 / 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 / 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 / SAD / Resolution: 1.45 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: J.Am.Chem.Soc. / Year: 2023
Title: High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST.
Authors: Rothfuss, M.T. / Becht, D.C. / Zeng, B. / McClelland, L.J. / Yates-Hansen, C. / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_seq_num / _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 2.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)5,6262
Polymers5,5341
Non-polymers921
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.164, 31.164, 40.530
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: 5534.243 Da / Num. of mol.: 1 / Mutation: Y188G
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.7830.83
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop2.0M Ammonium sulfate
2932vapor diffusion, sitting drop2.0M Ammonium sulfate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9795
SYNCHROTRONSSRL BL9-221.77
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJan 29, 2020
DECTRIS PILATUS 6M2PIXELJan 29, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.771
Reflection

Entry-ID: 6W2I / CC1/2: 1 / CC star: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.45-31.16687598.9513.411.230.076580.021530.07961122.37
1.9-31.14308399.143.516.480.037590.0055480.03801293.75
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allDiffraction-ID% possible all
1.45-1.50212.50.59014.346800.9260.980.17030.615197.84
1.9-1.96824.10.0913529.742920.99910.01890.09335296.05

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
HKL2Map0.4.e-betaphasing
AutoSolphasing
PHENIX1.17.1-3660model building
Coot0.8.9.2 ELmodel building
PHENIX1.17.1-3660refinement
RefinementMethod to determine structure: SAD / Resolution: 1.45→31.16 Å / SU ML: 0.1067 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1748
RfactorNum. reflection% reflection
Rfree0.183 697 10.14 %
Rwork0.1498 --
obs0.1532 6875 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.14 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms369 0 6 48 423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112388
X-RAY DIFFRACTIONf_angle_d1.0683524
X-RAY DIFFRACTIONf_chiral_restr0.090459
X-RAY DIFFRACTIONf_plane_restr0.006868
X-RAY DIFFRACTIONf_dihedral_angle_d6.32860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.560.19391340.15131223X-RAY DIFFRACTION98.19
1.56-1.720.1921400.14351222X-RAY DIFFRACTION99.05
1.72-1.970.19371400.14271229X-RAY DIFFRACTION98.92
1.97-2.480.17741430.14391248X-RAY DIFFRACTION99.78
2.48-31.160.17871400.15651256X-RAY DIFFRACTION98.87

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