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- PDB-9ptf: Stabilized Y188N variant of the internal UBA Domain of HHR23A in ... -

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Basic information

Entry
Database: PDB / ID: 9ptf
TitleStabilized Y188N variant of the internal UBA Domain of HHR23A in the P43 space group
ComponentsUV excision repair protein RAD23 homolog A
KeywordsTRANSCRIPTION / three-helix bundle / stabilized variant / DNA excision repair
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / histone H4K20 demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / ubiquitin-specific protease binding / proteasome binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / proteasome complex / positive regulation of cell cycle / Josephin domain DUBs ...regulation of proteasomal ubiquitin-dependent protein catabolic process / histone H4K20 demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / ubiquitin-specific protease binding / proteasome binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / proteasome complex / positive regulation of cell cycle / Josephin domain DUBs / ubiquitin binding / protein destabilization / nucleotide-excision repair / 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 / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / 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
Lysine-specific demethylase RAD23A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRothfuss, M.T. / Lanchy, J.M. / Bowler, B.E. / Yates-Hansen, C.K. / McClelland, L.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM148610 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 United States
CitationJournal: To Be Published
Title: Stabilized Y188N variant of the internal UBA Domain of HHR23A in the P43 space group
Authors: Rothfuss, M.T. / Lanchy, J.M. / Bowler, B.E. / Yates-Hansen, C.K. / McClelland, L.J.
History
DepositionJul 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)5,5911
Polymers5,5911
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.240, 31.240, 40.308
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: 5591.294 Da / Num. of mol.: 1
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.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.76 Å3/Da / Density % sol: 30.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate (pH 6.5), 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.198→24.69 Å / Num. obs: 60759 / % possible obs: 90.86 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.03 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07213 / Rpim(I) all: 0.03105 / Rrim(I) all: 0.07871 / Net I/σ(I): 10.37
Reflection shellResolution: 1.198→1.241 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.5989 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 4947 / CC1/2: 0.92 / CC star: 0.979 / Rpim(I) all: 0.2803 / Rrim(I) all: 0.6638

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→24.69 Å / SU ML: 0.0665 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 555 4.99 %
Rwork0.192 10563 -
obs0.1931 11118 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.92 Å2
Refinement stepCycle: LAST / Resolution: 1.2→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms390 0 0 30 420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052395
X-RAY DIFFRACTIONf_angle_d0.6334535
X-RAY DIFFRACTIONf_chiral_restr0.057162
X-RAY DIFFRACTIONf_plane_restr0.005370
X-RAY DIFFRACTIONf_dihedral_angle_d23.5986148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.320.30661280.29792477X-RAY DIFFRACTION86.23
1.32-1.510.26111440.24662655X-RAY DIFFRACTION91.95
1.51-1.90.20651550.23042739X-RAY DIFFRACTION94.14
1.9-24.690.20021280.16452692X-RAY DIFFRACTION91.06

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