[English] 日本語
Yorodumi
- PDB-4yir: Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA -

+
Open data


ID or keywords:

Loading...

-
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 / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding ...PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / ERAD pathway / ubiquitin binding / nucleotide-excision repair / protein-macromolecule adaptor activity / single-stranded DNA binding / 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 / Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / 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 BHD1 / Rad4, beta-hairpin domain BHD2 / XPC-binding domain / Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / 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 / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Anthopleurin-A / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more