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- PDB-6j0y: Crystal Structure of Yeast Rtt107 and Slx4 -

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Basic information

Entry
Database: PDB / ID: 6j0y
TitleCrystal Structure of Yeast Rtt107 and Slx4
Components
  • Peptide from Structure-specific endonuclease subunit SLX4
  • Regulator of Ty1 transposition protein 107
KeywordsPROTEIN BINDING / BRCT domain / mitosis / protein interaction
Function / homology
Function and homology information


regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / double-strand break repair via single-strand annealing, removal of nonhomologous ends / regulation of DNA double-strand break processing / Slx1-Slx4 complex / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / 5'-flap endonuclease activity / retrotransposon silencing / regulation of DNA damage checkpoint / double-strand break repair via break-induced replication ...regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / double-strand break repair via single-strand annealing, removal of nonhomologous ends / regulation of DNA double-strand break processing / Slx1-Slx4 complex / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / 5'-flap endonuclease activity / retrotransposon silencing / regulation of DNA damage checkpoint / double-strand break repair via break-induced replication / interstrand cross-link repair / cell periphery / DNA-templated DNA replication / double-strand break repair / nucleosome assembly / DNA replication / DNA damage response / nucleus / cytoplasm
Similarity search - Function
Structure-specific endonuclease subunit Slx4, ascomycetes / Regulator of Ty1 transposition protein 107, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. ...Structure-specific endonuclease subunit Slx4, ascomycetes / Regulator of Ty1 transposition protein 107, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / 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 / Structure-specific endonuclease subunit SLX4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 107
C: Peptide from Structure-specific endonuclease subunit SLX4
B: Regulator of Ty1 transposition protein 107
D: Peptide from Structure-specific endonuclease subunit SLX4


Theoretical massNumber of molelcules
Total (without water)131,7484
Polymers131,7484
Non-polymers00
Water14,250791
1
A: Regulator of Ty1 transposition protein 107
C: Peptide from Structure-specific endonuclease subunit SLX4


Theoretical massNumber of molelcules
Total (without water)65,8742
Polymers65,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-16 kcal/mol
Surface area23490 Å2
MethodPISA
2
B: Regulator of Ty1 transposition protein 107
D: Peptide from Structure-specific endonuclease subunit SLX4


Theoretical massNumber of molelcules
Total (without water)65,8742
Polymers65,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-11 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.450, 77.950, 78.380
Angle α, β, γ (deg.)89.950, 79.150, 83.970
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 59315.852 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 from Structure-specific endonuclease subunit SLX4


Mass: 6558.275 Da / Num. of mol.: 2 / Fragment: Rtt107 interacting motif 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SLX4, YLR135W, L3140 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12098
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.87 Å3/Da / Density % sol: 57.16 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 7
Details: 10% PEG 6000, 0.1M HEPES pH 7.0, silver bullets additive G9

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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: May 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.79→55.15 Å / Num. obs: 134886 / % possible obs: 97.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Net I/σ(I): 15 / Num. measured all: 532667
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
1.79-1.8440.6723905998050.8470.3890.7772.196.1
8.01-55.153.60.03544215070.9970.0190.03639.197.5

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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: 1.8→35.873 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 6498 4.9 %
Rwork0.1593 126152 -
obs0.1605 132650 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.31 Å2 / Biso mean: 40.156 Å2 / Biso min: 14.57 Å2
Refinement stepCycle: final / Resolution: 1.8→35.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8681 0 0 791 9472
Biso mean---44.75 -
Num. residues----1060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.28782020.26284206440896
1.8205-1.84190.27772120.24364105431796
1.8419-1.86430.27292190.23274192441196
1.8643-1.88790.24192200.22114057427796
1.8879-1.91280.22782040.21934205440996
1.9128-1.9390.21962020.21244172437497
1.939-1.96670.22392320.20134153438596
1.9667-1.9960.23991930.19234171436497
1.996-2.02720.23672040.19534223442797
2.0272-2.06040.2192040.19064189439397
2.0604-2.0960.22132570.17514074433197
2.096-2.13410.21162510.16674180443197
2.1341-2.17510.18262280.16144204443297
2.1751-2.21950.16972500.16164166441697
2.2195-2.26780.20522110.16144203441498
2.2678-2.32050.17882180.15864148436697
2.3205-2.37850.21522200.16324241446198
2.3785-2.44280.19851890.17094281447098
2.4428-2.51470.23752170.17114227444498
2.5147-2.59580.2012140.16974162437698
2.5958-2.68860.2111920.16834299449198
2.6886-2.79620.19532020.17514226442898
2.7962-2.92340.20952400.17264206444698
2.9234-3.07740.1982270.17224234446199
3.0774-3.27010.20732120.16624292450499
3.2701-3.52240.20672120.16484279449199
3.5224-3.87650.15742360.1454223445999
3.8765-4.43660.14122140.12534270448499
4.4366-5.58620.12571860.12024341452799
5.5862-35.88040.15692300.14834223445398
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)
11.4778-0.07080.070.8388-0.09420.7530.02190.27220.1247-0.0414-0.04580.0666-0.0836-0.0290.01490.18750.05030.02640.20220.08550.2296-35.86-175.30420.038
23.2079-0.0562-0.49762.12050.03493.8285-0.0287-0.220.27080.21430.0275-0.0543-0.27530.0854-0.00760.25630.0319-0.00370.20170.06490.3022-21.287-174.36540.095
31.2748-0.55110.2751.7416-0.58731.13190.0003-0.0318-0.15910.0753-0.0462-0.07980.08380.08810.03850.22820.0023-0.01730.18540.09070.2729-5.119-210.88146.725
44.57211.1735-1.23813.5239-0.73823.0710.092-0.43090.35630.5495-0.0563-0.0764-0.19480.00330.01020.33820.013-0.02860.27310.08110.2939-11.912-186.71250.906
50.6512-0.30870.19760.5505-0.25090.40520.01010.04240.00870.0775-0.0589-0.0182-0.03870.00790.03560.28310.01130.02110.27350.0580.3289-22.11-189.51833.547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:486 )A1 - 486
2X-RAY DIFFRACTION2( CHAIN C AND RESID 530:587 )C530 - 587
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:486 )B1 - 486
4X-RAY DIFFRACTION4( CHAIN D AND RESID 535:587 )D535 - 587
5X-RAY DIFFRACTION5( CHAIN A AND RESID 601:998 ) OR ( CHAIN C AND RESID 601:649 ) OR ( CHAIN B AND RESID 601:901 ) OR ( CHAIN D AND RESID 601:643 )A601 - 998
6X-RAY DIFFRACTION5( CHAIN A AND RESID 601:998 ) OR ( CHAIN C AND RESID 601:649 ) OR ( CHAIN B AND RESID 601:901 ) OR ( CHAIN D AND RESID 601:643 )C601 - 649
7X-RAY DIFFRACTION5( CHAIN A AND RESID 601:998 ) OR ( CHAIN C AND RESID 601:649 ) OR ( CHAIN B AND RESID 601:901 ) OR ( CHAIN D AND RESID 601:643 )B601 - 901
8X-RAY DIFFRACTION5( CHAIN A AND RESID 601:998 ) OR ( CHAIN C AND RESID 601:649 ) OR ( CHAIN B AND RESID 601:901 ) OR ( CHAIN D AND RESID 601:643 )D601 - 643

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