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- PDB-6j0w: Crystal Structure of Yeast Rtt107 and Nse6 -

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Basic information

Entry
Database: PDB / ID: 6j0w
TitleCrystal Structure of Yeast Rtt107 and Nse6
Components
  • Peptide from DNA repair protein KRE29
  • Regulator of Ty1 transposition protein 107
KeywordsPROTEIN BINDING / BRCT domain / mitosis / protein interaction
Function / homology
Function and homology information


regulation of DNA double-strand break processing / Smc5-Smc6 complex / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / regulation of DNA damage checkpoint / chromatin looping / regulation of telomere maintenance / protein sumoylation / cell periphery ...regulation of DNA double-strand break processing / Smc5-Smc6 complex / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / regulation of DNA damage checkpoint / chromatin looping / regulation of telomere maintenance / protein sumoylation / cell periphery / double-strand break repair via homologous recombination / double-strand break repair / nucleosome assembly / chromosome, telomeric region / DNA repair / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Regulator of Ty1 transposition protein 107, BRCT domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6 / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. ...Regulator of Ty1 transposition protein 107, BRCT domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6 / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
Regulator of Ty1 transposition protein 107 / DNA repair protein KRE29
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWan, B. / Wu, J. / Lei, M.
CitationJournal: Mol.Cell / Year: 2019
Title: Molecular Basis for Control of Diverse Genome Stability Factors by the Multi-BRCT Scaffold Rtt107.
Authors: Wan, B. / Wu, J. / Meng, X. / Lei, M. / Zhao, X.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 107
B: Regulator of Ty1 transposition protein 107
C: Peptide from DNA repair protein KRE29
D: Peptide from DNA repair protein KRE29


Theoretical massNumber of molelcules
Total (without water)125,0424
Polymers125,0424
Non-polymers00
Water90150
1
A: Regulator of Ty1 transposition protein 107
C: Peptide from DNA repair protein KRE29


Theoretical massNumber of molelcules
Total (without water)62,5212
Polymers62,5212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-10 kcal/mol
Surface area21860 Å2
MethodPISA
2
B: Regulator of Ty1 transposition protein 107
D: Peptide from DNA repair protein KRE29


Theoretical massNumber of molelcules
Total (without water)62,5212
Polymers62,5212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-9 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.777, 101.418, 86.559
Angle α, β, γ (deg.)90.000, 108.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Regulator of Ty1 transposition protein 107 / Establishes silent chromatin protein 4


Mass: 59359.969 Da / Num. of mol.: 2 / Fragment: NTD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RTT107, ESC4, YHR154W / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38850
#2: Protein/peptide Peptide from DNA repair protein KRE29 / Killer toxin-resistance protein 29


Mass: 3161.279 Da / Num. of mol.: 2 / Fragment: Rtt107 interacting motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: KRE29, YER038C / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40026
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.5 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 6
Details: 22% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97855 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.4→82.05 Å / Num. obs: 46118 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.052 / Rrim(I) all: 0.1 / Net I/σ(I): 12.1 / Num. measured all: 173636
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.773.80.48461335161120.850.2880.5643.199.9
4.79-82.053.60.0412104558190.9970.0250.04827.399.1

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J0V

6j0v


Resolution: 2.4→45.707 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 2248 4.9 %
Rwork0.2182 43603 -
obs0.2208 45851 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.82 Å2 / Biso mean: 48.8934 Å2 / Biso min: 9.36 Å2
Refinement stepCycle: final / Resolution: 2.4→45.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7913 0 0 50 7963
Biso mean---33.87 -
Num. residues----968
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.45220.37211450.30227122857100
2.4522-2.50920.34121310.276127142845100
2.5092-2.5720.33781440.276727342878100
2.572-2.64150.34331420.269227212863100
2.6415-2.71920.37531430.261527112854100
2.7192-2.8070.32381300.255627122842100
2.807-2.90730.3611280.252727672895100
2.9073-3.02370.34121290.248127312860100
3.0237-3.16120.2611330.2327192852100
3.1612-3.32790.30711540.229927302884100
3.3279-3.53630.291330.225127092842100
3.5363-3.80920.27151510.22072718286999
3.8092-4.19230.25751460.20072705285199
4.1923-4.79840.20291610.17072725288699
4.7984-6.04330.21121350.190327492884100
6.0433-45.7150.23131430.19392746288998
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)
10.0196-0.08830.0071.23760.86671.0988-0.10330.04950.0017-0.04660.17440.0035-0.09280.0264-00.03830.03610.01630.09420.00590.101742.44579.798112.105
20.56360.20840.59670.820.27790.67240.0562-0.0348-0.03620.06090.14190.16920.0754-0.105700.1874-0.03250.01260.22410.08640.212961.81780.496149.093
3-0.01-0.00910.01830.0077-0.01350.0013-0.11560.150.0150.0108-0.0855-0.1001-0.23980.0633-00.67-0.11820.04860.51710.01690.488654.3486.73799.944
40.0211-0.0705-0.00680.0429-0.06360.0155-0.0538-0.0069-0.1602-0.17470.1126-0.00520.2478-0.198400.6738-0.0639-0.04880.5606-0.15480.54977.70173.233145.463
5-0.0249-0.08350.05120.0221-0.00140.0109-0.1410.00120.06360.22290.08390.0227-0.0954-0.0753-0-0.1469-0.0720.0590.17950.01390.136752.86278.63131.376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:484 )A2 - 484
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:484 )B2 - 484
3X-RAY DIFFRACTION3( CHAIN C AND RESID 13:39 )C13 - 39
4X-RAY DIFFRACTION4( CHAIN D AND RESID 13:41 )D13 - 41
5X-RAY DIFFRACTION5( CHAIN A AND RESID 601:626 ) OR ( CHAIN C AND RESID 101:102 ) OR ( CHAIN B AND RESID 601:618 ) OR ( CHAIN D AND RESID 101:104 )A601 - 626
6X-RAY DIFFRACTION5( CHAIN A AND RESID 601:626 ) OR ( CHAIN C AND RESID 101:102 ) OR ( CHAIN B AND RESID 601:618 ) OR ( CHAIN D AND RESID 101:104 )C101 - 102
7X-RAY DIFFRACTION5( CHAIN A AND RESID 601:626 ) OR ( CHAIN C AND RESID 101:102 ) OR ( CHAIN B AND RESID 601:618 ) OR ( CHAIN D AND RESID 101:104 )B601 - 618
8X-RAY DIFFRACTION5( CHAIN A AND RESID 601:626 ) OR ( CHAIN C AND RESID 101:102 ) OR ( CHAIN B AND RESID 601:618 ) OR ( CHAIN D AND RESID 101:104 )D101 - 104

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