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

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Basic information

Entry
Database: PDB / ID: 9pte
TitleStabilized Y188N variant of the internal UBA Domain of HHR23A in the P1 21 1 space group
ComponentsUV excision repair protein RAD23 homolog A
KeywordsTRANSCRIPTION / Three-helix bundle / DNA excision repair / stabilized variant
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: 1.15 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 P1 21 1 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
B: UV excision repair protein RAD23 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2793
Polymers11,1832
Non-polymers961
Water2,306128
1
A: UV excision repair protein RAD23 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6872
Polymers5,5911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UV excision repair protein RAD23 homolog A


Theoretical massNumber of molelcules
Total (without water)5,5911
Polymers5,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.714, 40.497, 31.703
Angle α, β, γ (deg.)90.000, 90.378, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein UV excision repair protein RAD23 homolog A / HR23A / hHR23A


Mass: 5591.294 Da / Num. of mol.: 2
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: 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.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 30.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris (pH 5.5), 25% w/v PEG3350

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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: 1.15→31.7 Å / Num. obs: 57209 / % possible obs: 95.96 % / Redundancy: 2.1 % / Biso Wilson estimate: 5.87 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.04866 / Rpim(I) all: 0.0375 / Rrim(I) all: 0.06174 / Net I/σ(I): 12.33
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.1071 / Mean I/σ(I) obs: 4.66 / Num. unique obs: 796 / CC1/2: 0.967 / CC star: 0.992 / Rpim(I) all: 0.1048 / Rrim(I) all: 0.15 / % possible all: 74.92

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→31.7 Å / SU ML: 0.0691 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 15.1801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1633 1249 4.69 %
Rwork0.153 25363 -
obs0.1534 26612 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.99 Å2
Refinement stepCycle: LAST / Resolution: 1.15→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 5 128 913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066794
X-RAY DIFFRACTIONf_angle_d0.93151076
X-RAY DIFFRACTIONf_chiral_restr0.0749124
X-RAY DIFFRACTIONf_plane_restr0.0094140
X-RAY DIFFRACTIONf_dihedral_angle_d16.8015296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.20.17831160.14852241X-RAY DIFFRACTION76.5
1.2-1.250.16581610.14142763X-RAY DIFFRACTION96.31
1.25-1.320.16291380.142899X-RAY DIFFRACTION98.96
1.32-1.40.15561690.14082862X-RAY DIFFRACTION98.44
1.4-1.510.16571310.1392880X-RAY DIFFRACTION98.3
1.51-1.660.15631380.13662904X-RAY DIFFRACTION99.12
1.66-1.90.153950.15022951X-RAY DIFFRACTION98.64
1.9-2.390.16271510.15592914X-RAY DIFFRACTION99.09
2.39-31.70.16751500.17072949X-RAY DIFFRACTION98.23

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