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- PDB-7tgp: E176T/Y188G variant of the internal UBA Domain of HHR23A -

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Basic information

Entry
Database: PDB / ID: 7tgp
TitleE176T/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 / 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: 1.4 Å
AuthorsRothfuss, M. / Bowler, B.E. / McClelland, L.J. / Sprang, S.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1904895 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 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
DepositionJan 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 1, 2023Group: 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

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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


Theoretical massNumber of molelcules
Total (without water)5,5061
Polymers5,5061
Non-polymers00
Water52229
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)31.120, 31.120, 40.208
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 / HR23A / hHR23A


Mass: 5506.233 Da / Num. of mol.: 1 / Fragment: residues 154-204 of the Internal UBA domain / Mutation: E176T, Y188G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54725
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.77 Å3/Da / Density % sol: 30.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→31.12 Å / Num. obs: 7624 / % possible obs: 99.82 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.78 Å2 / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 754 / CC1/2: 0.604 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874model building
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w2g

6w2g


Resolution: 1.4→31.12 Å / SU ML: 0.1046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.9042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1747 360 4.73 %
Rwork0.1605 7256 -
obs0.1613 7616 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms384 0 0 29 413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037389
X-RAY DIFFRACTIONf_angle_d0.4989527
X-RAY DIFFRACTIONf_chiral_restr0.049262
X-RAY DIFFRACTIONf_plane_restr0.002868
X-RAY DIFFRACTIONf_dihedral_angle_d12.1119144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.60.24871170.2352398X-RAY DIFFRACTION99.64
1.6-2.020.18961260.18492405X-RAY DIFFRACTION99.88
2.02-31.120.15841170.142453X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 12.057707872 Å / Origin y: 0.453982587344 Å / Origin z: -4.26565807047 Å
111213212223313233
T0.105179210861 Å2-0.00507474447896 Å20.00480703252141 Å2-0.117430404463 Å2-0.00633862239937 Å2--0.0981912465695 Å2
L2.99918005977 °2-0.438547615668 °21.39525398848 °2-1.12279260111 °2-0.524380367249 °2--3.70553223894 °2
S0.042389680563 Å °0.0547912713158 Å °0.00179891965139 Å °0.0105756098874 Å °0.0099586457812 Å °-0.0244495169493 Å °-0.0400108921861 Å °0.142715331389 Å °-0.0624683052777 Å °
Refinement TLS groupSelection details: all

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