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- PDB-6j0x: Crystal Structure of Yeast Rtt107 and Mms22 -

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Basic information

Entry
Database: PDB / ID: 6j0x
TitleCrystal Structure of Yeast Rtt107 and Mms22
Components
  • Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22
  • 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 / meiotic sister chromatid segregation / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / regulation of DNA damage checkpoint / recombinational repair / replication fork processing / cell periphery / double-strand break repair via homologous recombination ...regulation of DNA double-strand break processing / meiotic sister chromatid segregation / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / regulation of DNA damage checkpoint / recombinational repair / replication fork processing / cell periphery / double-strand break repair via homologous recombination / double-strand break repair / nucleosome assembly / cell division / chromatin binding / DNA damage response / nucleus
Similarity search - Function
E3 ubiquitin-protein ligase substrate receptor Mms22, budding yeast / E3 ubiquitin-protein ligase substrate receptor Mms22 / Mus7/MMS22 family / 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...E3 ubiquitin-protein ligase substrate receptor Mms22, budding yeast / E3 ubiquitin-protein ligase substrate receptor Mms22 / Mus7/MMS22 family / 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 / 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 / E3 ubiquitin-protein ligase substrate receptor MMS22
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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
E: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22
B: Regulator of Ty1 transposition protein 107
F: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22
C: Regulator of Ty1 transposition protein 107
G: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22
D: Regulator of Ty1 transposition protein 107
H: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22


Theoretical massNumber of molelcules
Total (without water)245,5088
Polymers245,5088
Non-polymers00
Water5,855325
1
A: Regulator of Ty1 transposition protein 107
E: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22


Theoretical massNumber of molelcules
Total (without water)61,3772
Polymers61,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area22110 Å2
MethodPISA
2
B: Regulator of Ty1 transposition protein 107
F: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22


Theoretical massNumber of molelcules
Total (without water)61,3772
Polymers61,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-11 kcal/mol
Surface area22130 Å2
MethodPISA
3
C: Regulator of Ty1 transposition protein 107
G: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22


Theoretical massNumber of molelcules
Total (without water)61,3772
Polymers61,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-11 kcal/mol
Surface area22050 Å2
MethodPISA
4
D: Regulator of Ty1 transposition protein 107
H: Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22


Theoretical massNumber of molelcules
Total (without water)61,3772
Polymers61,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-12 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.284, 99.669, 167.057
Angle α, β, γ (deg.)90.000, 94.920, 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.: 4 / 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 E3 ubiquitin-protein ligase substrate receptor MMS22 / Methyl methanesulfonate-sensitivity protein 22 / Synthetically lethal with MCM10 protein 2


Mass: 2017.151 Da / Num. of mol.: 4 / 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: MMS22, SLM2, YLR320W / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06164
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.44 Å3/Da / Density % sol: 49.63 % / Mosaicity: 0.14 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 6
Details: 25% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.2M magnesium chloride

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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: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.31→166.44 Å / Num. obs: 102743 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 35.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.049 / Rrim(I) all: 0.099 / Net I/σ(I): 14.2 / Num. measured all: 403753
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
2.31-2.352.20.9821111249560.3210.861.312197.1
12.65-166.443.90.0226386760.9990.0110.02348.199.3

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J0V

6j0v


Resolution: 2.31→49.433 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 5083 4.95 %
Rwork0.2036 97565 -
obs0.2053 102648 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.56 Å2 / Biso mean: 45.2902 Å2 / Biso min: 13.27 Å2
Refinement stepCycle: final / Resolution: 2.31→49.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15804 0 0 325 16129
Biso mean---37.75 -
Num. residues----1920
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 (%)
2.31-2.33630.36021580.36253174333296
2.3363-2.36370.33691790.32643163334297
2.3637-2.39260.34541750.31813187336299
2.3926-2.42280.31021710.2953239341099
2.4228-2.45470.3141480.30033260340899
2.4547-2.48840.2961700.27593239340999
2.4884-2.52390.31461620.270432193381100
2.5239-2.56160.31471660.27543261342798
2.5616-2.60160.32321750.258632313406100
2.6016-2.64420.28621820.24843194337699
2.6442-2.68980.29841750.23283264343999
2.6898-2.73880.25921620.237832733435100
2.7388-2.79140.27381690.22383238340799
2.7914-2.84840.27411770.22993228340599
2.8484-2.91030.27691800.225732603440100
2.9103-2.9780.27141830.2223223340699
2.978-3.05250.29031720.22753200337299
3.0525-3.1350.27961800.23193278345899
3.135-3.22720.24771500.21773258340899
3.2272-3.33140.25581800.21743252343299
3.3314-3.45040.24591640.19723248341299
3.4504-3.58850.24181450.19473288343399
3.5885-3.75180.23261660.18453263342999
3.7518-3.94950.22211700.18173250342099
3.9495-4.19680.2071770.16823278345599
4.1968-4.52070.17351440.150733673511100
4.5207-4.97520.17811610.154532633424100
4.9752-5.69430.17371710.166733093480100
5.6943-7.17070.20791960.17132993495100
7.1707-49.44440.17391750.15623359353499
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)
10.011-0.088-0.0840.33650.24690.5456-0.04320.0401-0.0170.08130.00780.03290.0432-0.049500.1339-0.0212-0.00490.1623-0.01580.164727.602-80.47252.921
20.0005-0.0084-0.00180.0009-0.01780.00250.1622-0.0750.0390.11960.07630.02590.09710.010400.35140.0076-0.0440.3612-0.03630.240537.349-81.1169.516
30.1646-0.1144-0.2580.28760.06040.75480.05370.01280.0065-0.1094-0.0093-0.0449-0.0682-0.073700.22870.0137-0.00240.20090.02180.212746.09-80.75315.857
40.00480.0134-0.00440.0007-0.00750.01020.02430.1021-0.011-0.0754-0.0951-0.15010.03970.096800.2986-0.01160.05820.3206-0.00250.32965.35-80.03613.952
50.0612-0.2068-0.01440.7546-0.27740.5686-0.0494-0.0811-0.0178-0.12340.12550.06780.06590.049900.17890.0008-0.01330.18140.01870.192475.638-129.89130.63
60.00280.0003-0.0010.00270.0053-0.01030.14230.1647-0.0158-0.1745-0.06960.09960.05-0.0535-00.4015-0.0242-0.08760.3446-0.02390.344465.059-130.60414.562
70.34940.154-0.07790.74370.10450.1287-0.0040.00630.0121-0.04210.108-0.018-0.05650.046500.1754-0.02420.00670.1952-0.02390.175956.944-131.80369.408
80.0103-0.0339-0.004-0.00220.00960.00910.1623-0.0783-0.0864-0.14160.06690.0528-0.0076-0.02930-0.07060.12510.01150.26320.06190.341637.998-129.93367.826
9-0.0062-0.06010.020.1571-0.07070.08730.0146-0.0204-0.014-0.0385-0.00150.04760.0058-0.013600.0594-0.0073-0.00330.1139-0.00140.110840.232-97.82947.43
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 E AND RESID 22:37 )E22 - 37
3X-RAY DIFFRACTION3( CHAIN B AND RESID 2:485 )B2 - 485
4X-RAY DIFFRACTION4( CHAIN F AND RESID 22:37 )F22 - 37
5X-RAY DIFFRACTION5( CHAIN C AND RESID 2:485 )C2 - 485
6X-RAY DIFFRACTION6( CHAIN G AND RESID 22:37 )G22 - 37
7X-RAY DIFFRACTION7( CHAIN D AND RESID 2:485 )D2 - 485
8X-RAY DIFFRACTION8( CHAIN H AND RESID 22:37 )H22 - 37
9X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )A601 - 727
10X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )C601 - 625
11X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )B601 - 682
12X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )E101 - 105
13X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )D601 - 680
14X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )G101
15X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )F101 - 102
16X-RAY DIFFRACTION9( CHAIN A AND RESID 601:727 ) OR ( CHAIN C AND RESID 601:625 ) OR ( CHAIN B AND RESID 601:682 ) OR ( CHAIN E AND RESID 101:105 ) OR ( CHAIN D AND RESID 601:680 ) OR ( CHAIN G AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:102 ) OR ( CHAIN H AND RESID 101:103 )H101 - 103

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