[English] 日本語
Yorodumi
- PDB-8b4j: Rfa1-N-terminal domain in complex with phosphorylated Ddc2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b4j
TitleRfa1-N-terminal domain in complex with phosphorylated Ddc2
Components
  • DNA damage checkpoint protein LCD1
  • Replication factor A protein 1
KeywordsPROTEIN BINDING / Complex / OB-fold / Replication Protein A / DNA damage response / Replication
Function / homology
Function and homology information


heteroduplex formation / ATR-ATRIP complex / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Removal of the Flap Intermediate / telomere maintenance via telomere lengthening / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK ...heteroduplex formation / ATR-ATRIP complex / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Removal of the Flap Intermediate / telomere maintenance via telomere lengthening / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Termination of translesion DNA synthesis / Activation of ATR in response to replication stress / single-stranded telomeric DNA binding / telomere maintenance via recombination / regulation of double-strand break repair / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / DNA damage checkpoint signaling / condensed nuclear chromosome / meiotic cell cycle / nucleotide-excision repair / establishment of protein localization / double-strand break repair via homologous recombination / single-stranded DNA binding / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / damaged DNA binding / chromosome, telomeric region / DNA replication / protein ubiquitination / DNA repair / mRNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type ...DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication factor A protein 1 / DNA damage checkpoint protein LCD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsYates, L.A. / Zhang, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210658/Z/18/Z United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A.
Authors: Yates, L.A. / Tannous, E.A. / Morgan, R.M. / Burgers, P.M. / Zhang, X.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: Replication factor A protein 1
P: DNA damage checkpoint protein LCD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0486
Polymers17,7902
Non-polymers2584
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-69 kcal/mol
Surface area7220 Å2
Unit cell
Length a, b, c (Å)39.996, 39.996, 282.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11O-332-

HOH

21O-349-

HOH

-
Components

#1: Protein Replication factor A protein 1 / RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / ...RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / Single-stranded DNA-binding protein


Mass: 15382.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RFA1, BUF2, RPA1, YAR007C, FUN3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 / References: UniProt: P22336
#2: Protein/peptide DNA damage checkpoint protein LCD1 / DNA damage checkpoint protein 2 / Lethal / checkpoint-defective / DNA damage-sensitive protein 1


Mass: 2407.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LCD1, DDC2, PIE1, YDR499W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04377
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 mM Zinc Chloride, 0.1M MES, pH 6.0, 20% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.58→56.4 Å / Num. obs: 19852 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.22 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.8
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 1878 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMB

5omb


Resolution: 1.58→47.01 Å / SU ML: 0.1652 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 1001 5.09 %
Rwork0.1912 18672 -
obs0.1933 19673 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.19 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 7 72 1188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421127
X-RAY DIFFRACTIONf_angle_d1.6241521
X-RAY DIFFRACTIONf_chiral_restr0.0676173
X-RAY DIFFRACTIONf_plane_restr0.0158198
X-RAY DIFFRACTIONf_dihedral_angle_d15.3335158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.660.28211220.22552607X-RAY DIFFRACTION100
1.66-1.770.25971360.2162548X-RAY DIFFRACTION100
1.77-1.90.22411540.20122617X-RAY DIFFRACTION100
1.9-2.10.23011250.19012636X-RAY DIFFRACTION100
2.1-2.40.21281390.18142650X-RAY DIFFRACTION100
2.4-3.020.24861480.19972714X-RAY DIFFRACTION100
3.02-47.010.22231770.18462900X-RAY DIFFRACTION98.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.08738139067-0.717127998813-0.3268173218952.83929216953-3.169331413626.167720674210.078098329312-0.2361901920170.174159445266-0.06825449830940.0819829319828-1.40435570301-0.396584723081.630054331540.06783619837220.162803637495-0.138000823160.001715336188480.38477553832-0.2038183856590.6926265576534.4453548201423.911482289111.3406514273
24.03695322898-0.859822348368-0.2686696963693.191720754760.4149217799715.10103776257-0.181042808354-0.3545757804570.207018754825-0.05675192216660.1194239466920.0168917716116-0.314531479732-0.02807831281060.06829042222920.08871548438790.0159170778602-0.01223708014330.149886149462-0.01945256605880.172038189184-7.9453322195222.011828588910.1335501436
30.347680526708-0.7977147860980.9396101886345.135305791111.245311721986.4440676898-0.0375120632015-0.788809784482-1.158338288840.356759033168-0.1100434102890.1795752084671.17658359433-0.161915760803-0.0486148528330.344023862130.05511772431780.08619333907490.2625814945460.1225193695780.590189149371-5.750724553084.6945125059612.5861592325
43.57451879946-0.798667828164-0.6748230673922.716943987110.7879439929323.36592594766-0.152118366622-0.151302215162-0.402699592554-0.08272675691210.01467462956890.002241067870720.4416019775240.2381855341340.09725892518570.1681999751460.04222754814940.02365175612680.1690621209280.04443282876030.246144067642-2.1614045558711.14043067937.89118152866
57.106570941022.78151741446-5.203871742675.24024393217-2.567892013774.49070313681-0.148515195223-0.851351890253-0.1767858930920.3440922596690.06939528437960.4279627337670.305494592032-0.05842230806840.1049537727610.1711175645220.03165460452370.03624641262960.4276552203750.07243387352690.309600970368-17.893359600114.873644391213.5447007368
64.69546868252-0.134827900063-0.5967736389312.336796464241.121122211656.10226376365-0.07267905974610.163492952013-0.407633671936-0.1314389175120.0353756382863-0.06157870797480.126309041235-0.1697675624180.1051246578330.1141016420230.0223302926970.001409082379180.06834201628080.02884317264410.187734350907-5.4670352618613.84319610196.59533691703
76.80279082785-2.43296698434-6.816144182331.487429280351.917468633617.3061016867-0.242487060575-1.18375420350.2430156560120.1851877553160.200852360315-0.8022947630780.3061449843531.585644009630.04278381643280.3201392772540.115672444765-0.02408217723150.6122414707640.02686020765620.3879131112674.3034612372415.895401302218.0348313656
87.08376423707-0.411038397439-1.306401847316.89851985128-1.279983236840.5173194623540.15609679399-0.3498550503010.3138686532990.100792787517-0.1785484731170.432910844339-0.236389595042-0.607289385005-0.05739209421690.1719385376050.09234460320940.00432936785060.484229426711-0.05126013585950.21527935983-13.987124962723.09040381122.4442174794
91.27547209085-0.448300028829-2.340102796853.80864888026-2.124361315396.65351789476-0.5381016618440.4412529275970.0133401696932-0.4638484299110.2240708135970.6023188652870.7644342978461.0422576965-0.00634072417820.419052031473-0.127908641235-0.100100199480.5781566230450.1234269112130.524966945363-15.82638220054.3867172023514.0723495064
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'O' and (resid 3 through 9 )OA3 - 91 - 7
22chain 'O' and (resid 10 through 33 )OA10 - 338 - 31
33chain 'O' and (resid 34 through 51 )OA34 - 5132 - 44
44chain 'O' and (resid 52 through 83 )OA52 - 8345 - 76
55chain 'O' and (resid 84 through 94 )OA84 - 9477 - 87
66chain 'O' and (resid 95 through 107 )OA95 - 10788 - 100
77chain 'O' and (resid 108 through 119 )OA108 - 119101 - 112
88chain 'O' and (resid 120 through 132 )OA120 - 132113 - 125
99chain 'P' and (resid 10 through 24 )PC10 - 241 - 15

+
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://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