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- PDB-8b4j: Rfa1-N-terminal domain in complex with phosphorylated Ddc2 -

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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 / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex ...heteroduplex formation / ATR-ATRIP complex / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / regulation of double-strand break repair / single-stranded telomeric DNA binding / Activation of ATR in response to replication stress / mitotic recombination / Termination of translesion DNA synthesis / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / DNA unwinding involved in DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / DNA damage checkpoint signaling / nucleotide-excision repair / double-strand break repair via homologous recombination / establishment of protein localization / chromatin organization / single-stranded DNA binding / double-stranded DNA binding / DNA replication / sequence-specific DNA binding / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / mRNA binding / nucleus / metal ion binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 1.83 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

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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

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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

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