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- PDB-3t7k: Complex structure of Rtt107p and phosphorylated histone H2A -

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Basic information

Entry
Database: PDB / ID: 3t7k
TitleComplex structure of Rtt107p and phosphorylated histone H2A
Components
  • Histone H2A.1
  • Regulator of Ty1 transposition protein 107
KeywordsPROTEIN BINDING / BRCT / DNA repair / phospho-peptide
Function / homology
Function and homology information


regulation of DNA double-strand break processing / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / transposable element silencing / regulation of DNA damage checkpoint ...regulation of DNA double-strand break processing / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / transposable element silencing / regulation of DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / Ub-specific processing proteases / cell periphery / structural constituent of chromatin / nucleosome / heterochromatin formation / double-strand break repair / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA repair / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Regulator of Ty1 transposition protein 107, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain ...Regulator of Ty1 transposition protein 107, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H2A.1 / Regulator of Ty1 transposition protein 107
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.028 Å
AuthorsLi, X. / Li, F. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of C-terminal Tandem BRCT Repeats of Rtt107 Protein Reveals Critical Role in Interaction with Phosphorylated Histone H2A during DNA Damage Repair
Authors: Li, X. / Liu, K. / Li, F. / Wang, J. / Huang, H. / Wu, J. / Shi, Y.
History
DepositionJul 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 107
C: Histone H2A.1
B: Regulator of Ty1 transposition protein 107
D: Histone H2A.1


Theoretical massNumber of molelcules
Total (without water)60,6324
Polymers60,6324
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regulator of Ty1 transposition protein 107
C: Histone H2A.1


Theoretical massNumber of molelcules
Total (without water)30,3162
Polymers30,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-11 kcal/mol
Surface area12400 Å2
MethodPISA
3
B: Regulator of Ty1 transposition protein 107
D: Histone H2A.1


Theoretical massNumber of molelcules
Total (without water)30,3162
Polymers30,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-10 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.517, 59.255, 85.890
Angle α, β, γ (deg.)78.36, 89.68, 73.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Regulator of Ty1 transposition protein 107 / Rtt107


Mass: 29388.227 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RTT107 / Production host: Escherichia coli (E. coli) / References: UniProt: P38850
#2: Protein/peptide Histone H2A.1


Mass: 927.912 Da / Num. of mol.: 2 / Fragment: phosphorylated C-terminal peptide / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04911
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.62 % / Mosaicity: 7.234 °
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14%(w/v) PEG 1500, 0.2M NaCl, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 2.9 % / Av σ(I) over netI: 11.69 / Number: 116925 / Rmerge(I) obs: 0.076 / Χ2: 1.17 / D res high: 2.03 Å / D res low: 50 Å / Num. obs: 39702 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.515094.510.0520.8052.9
4.375.5199.110.0541.0033
3.824.3799.210.0551.1463
3.473.8294.610.0631.3712.8
3.223.4796.710.0721.6412.9
3.033.2296.310.0831.7092.9
2.883.0396.610.0891.5283
2.762.8896.610.1061.3943
2.652.7696.510.1341.333
2.562.6596.410.1471.1273
2.482.5696.410.1721.0812.9
2.412.4896.810.2041.0473
2.342.4196.510.2291.0212.9
2.292.3496.210.2611.043
2.232.2996.410.3111.0273
2.192.2396.110.3371.0352.9
2.142.1996.610.3660.9733
2.12.149610.4351.062.9
2.072.196.310.4911.1082.9
2.032.0795.610.561.0152.9
ReflectionResolution: 2.028→50 Å / Num. all: 41142 / Num. obs: 39702 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 33.71 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.173 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.028-2.072.90.5619061.015195.6
2.07-2.12.90.49119981.108196.3
2.1-2.142.90.43519921.06196
2.14-2.1930.36620150.973196.6
2.19-2.232.90.33719171.035196.1
2.23-2.2930.31120241.027196.4
2.29-2.3430.26119681.04196.2
2.34-2.412.90.22919861.021196.5
2.41-2.4830.20420391.047196.8
2.48-2.562.90.17219291.081196.4
2.56-2.6530.14720241.127196.4
2.65-2.7630.13419631.33196.5
2.76-2.8830.10620191.394196.6
2.88-3.0330.08919461.528196.6
3.03-3.222.90.08320011.709196.3
3.22-3.472.90.07220241.641196.7
3.47-3.822.80.06319331.371194.6
3.82-4.3730.05520361.146199.2
4.37-5.5130.05420451.003199.1
5.51-502.90.05219370.805194.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å30.55 Å
Translation2.5 Å30.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.028→30.548 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7501 / SU ML: 0.28 / σ(F): 0.08 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1880 5.07 %random
Rwork0.218 ---
obs0.2201 37087 90 %-
all-41208 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.999 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 74.27 Å2 / Biso mean: 44.6295 Å2 / Biso min: 24.79 Å2
Baniso -1Baniso -2Baniso -3
1-16.6106 Å25.3224 Å22.681 Å2
2---4.1713 Å2-2.5205 Å2
3----12.4393 Å2
Refinement stepCycle: LAST / Resolution: 2.028→30.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 0 101 3972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083933
X-RAY DIFFRACTIONf_angle_d1.1335296
X-RAY DIFFRACTIONf_chiral_restr0.077622
X-RAY DIFFRACTIONf_plane_restr0.004657
X-RAY DIFFRACTIONf_dihedral_angle_d14.9951486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0285-2.1010.35441670.29463138330581
2.101-2.18510.31961910.26723334352585
2.1851-2.28450.3381680.25563323349185
2.2845-2.40490.28151900.24743360355087
2.4049-2.55550.29211860.25213465365189
2.5555-2.75270.32451990.24893542374191
2.7527-3.02950.29581950.24133681387694
3.0295-3.46730.23451780.22133817399596
3.4673-4.36640.21372020.17553760396297
4.3664-30.55140.21482040.19233787399197

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