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- PDB-4yir: Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA -

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Basic information

Entry
Database: PDB / ID: 4yir
TitleCrystal structure of Rad4-Rad23 crosslinked to an undamaged DNA
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3')
  • DNA repair protein RAD4
  • UV excision repair protein RAD23
KeywordsDNA BINDING PROTEIN/DNA / DNA damage repair / nucleotide excision repair / protein-DNA interactions / protein-DNA crosslinking / protein-DNA complex / xeroderma pigmentosum / beta-hairpin / transglutaminase domain / disulfide crosslinking / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair ...PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / ERAD pathway / ubiquitin binding / nucleotide-excision repair / single-stranded DNA binding / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Rad4, beta-hairpin domain BHD1 / Rad4, beta-hairpin domain BHD2 / XPC-binding domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily ...Rad4, beta-hairpin domain BHD1 / Rad4, beta-hairpin domain BHD2 / XPC-binding domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Anthopleurin-A / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Transglutaminase-like superfamily / UBA/TS-N domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Single Sheet / Papain-like cysteine peptidase superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein RAD4 / UV excision repair protein RAD23
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0501 Å
AuthorsMin, J.-H. / Chen, X. / Kim, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
The Searle Funds at The Chicago Community Trust United States
The Chancellor's Discovery Fund, University of Illinois at Chicago United States
Startup funding, University of Illinois at Chicago United States
CitationJournal: Nat Commun / Year: 2015
Title: Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.
Authors: Chen, X. / Velmurugu, Y. / Zheng, G. / Park, B. / Shim, Y. / Kim, Y. / Liu, L. / Van Houten, B. / He, C. / Ansari, A. / Min, J.H.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMar 11, 2015ID: 4U29
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD4
X: UV excision repair protein RAD23
W: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3')
Y: DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)95,1724
Polymers95,1724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-49 kcal/mol
Surface area34540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.405, 79.405, 404.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA repair protein RAD4


Mass: 62588.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD4, YER162C / Cell line (production host): High Five Cells (BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14736
#2: Protein UV excision repair protein RAD23


Mass: 17783.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD23, YEL037C, SYGP-ORF29 / Cell line (production host): High Five Cells (BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32628
#3: DNA chain DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3')


Mass: 7294.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')


Mass: 7505.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50mM BTP-HCl, 100mM NaCl, 14% isopropanol and 100mM calcium chloride
PH range: 6.8

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97919 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.05→39.7 Å / Num. obs: 45912 / % possible obs: 97.51 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.8
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.792 / Num. unique all: 1228 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QSH

2qsh


Resolution: 3.0501→39.7 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 3506 7.64 %
Rwork0.1923 --
obs0.197 45912 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.0501→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 939 0 0 5459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185666
X-RAY DIFFRACTIONf_angle_d1.6857823
X-RAY DIFFRACTIONf_dihedral_angle_d21.4982234
X-RAY DIFFRACTIONf_chiral_restr0.068851
X-RAY DIFFRACTIONf_plane_restr0.009834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.09190.3646830.33281097X-RAY DIFFRACTION64
3.0919-3.1360.36241130.29181452X-RAY DIFFRACTION83
3.136-3.18280.33161390.26711709X-RAY DIFFRACTION96
3.1828-3.23250.36471420.23891695X-RAY DIFFRACTION99
3.2325-3.28550.30421490.22031757X-RAY DIFFRACTION100
3.2855-3.34210.27621440.22111710X-RAY DIFFRACTION100
3.3421-3.40290.24141480.21911754X-RAY DIFFRACTION100
3.4029-3.46830.27411430.20691717X-RAY DIFFRACTION100
3.4683-3.5390.24611470.20681726X-RAY DIFFRACTION100
3.539-3.61590.28551480.221787X-RAY DIFFRACTION100
3.6159-3.70.25371470.20721686X-RAY DIFFRACTION100
3.7-3.79250.33511450.20831733X-RAY DIFFRACTION100
3.7925-3.89490.26671390.21581727X-RAY DIFFRACTION100
3.8949-4.00940.27751480.19531767X-RAY DIFFRACTION100
4.0094-4.13870.2131500.1831742X-RAY DIFFRACTION100
4.1387-4.28650.28241380.17651695X-RAY DIFFRACTION100
4.2865-4.45790.2931440.16791772X-RAY DIFFRACTION100
4.4579-4.66040.22961390.16331754X-RAY DIFFRACTION100
4.6604-4.90570.21921460.15951719X-RAY DIFFRACTION100
4.9057-5.21250.22161320.17071754X-RAY DIFFRACTION100
5.2125-5.61390.21731400.16831749X-RAY DIFFRACTION100
5.6139-6.1770.25311440.19061727X-RAY DIFFRACTION100
6.177-7.06640.22131490.18991725X-RAY DIFFRACTION100
7.0664-8.88650.19451430.16411748X-RAY DIFFRACTION100
8.8865-39.70580.21481460.17581704X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 35.4288 Å / Origin y: 28.4702 Å / Origin z: 437.0431 Å
111213212223313233
T0.3359 Å20.1538 Å20.2271 Å2-0.4583 Å2-0.0176 Å2--0.4545 Å2
L1.8657 °20.3728 °2-0.0736 °2-0.4432 °2-0.1515 °2--0.7009 °2
S0.1679 Å °-0.2325 Å °0.1952 Å °-0.0151 Å °-0.1177 Å °-0.2994 Å °0.0387 Å °0.0572 Å °-0.0329 Å °
Refinement TLS groupSelection details: all

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