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- PDB-7ogg: Nse5/6 complex -

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Basic information

Entry
Database: PDB / ID: 7ogg
TitleNse5/6 complex
Components
  • DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29
  • Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5
KeywordsDNA BINDING PROTEIN / NSe5/6
Function / homology
Function and homology information


Smc5-Smc6 complex / ATPase inhibitor activity / chromatin looping / regulation of telomere maintenance / double-strand break repair via homologous recombination / chromosome, telomeric region / DNA repair / nucleus / cytoplasm
Similarity search - Function
DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6
Similarity search - Domain/homology
DNA repair protein KRE29 / Non-structural maintenance of chromosome element 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae A364A (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.29 Å
AuthorsBasquin, J. / Taschner, M. / Gruber, S.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030L_170242 Switzerland
European Research Council (ERC)Horizon 2020 ERC CoG 724482
CitationJournal: Embo J. / Year: 2021
Title: Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding.
Authors: Taschner, M. / Basquin, J. / Steigenberger, B. / Schafer, I.B. / Soh, Y.M. / Basquin, C. / Lorentzen, E. / Raschle, M. / Scheltema, R.A. / Gruber, S.
History
DepositionMay 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5
Q: DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29


Theoretical massNumber of molelcules
Total (without water)105,1282
Polymers105,1282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-18 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.116, 147.368, 74.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5 / Non-SMC element 5


Mass: 68794.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Saccharomyces cerevisiae A364A (yeast)
Strain: ATCC 204508 / S288c / Gene: NSE5, YML023C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q03718
#2: Protein DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29 / Killer toxin-resistance protein 29


Mass: 36332.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae A364A (yeast) / Gene: KRE29, YER038C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P40026
Has ligand of interestN
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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% (w/v) PEG 3350, 8% (v/v) 0.3 M Sodium malonate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.29→19.85 Å / Num. all: 91905 / Num. obs: 16988 / % possible obs: 99.08 % / Redundancy: 5.4 % / Biso Wilson estimate: 110.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07468 / Net I/σ(I): 16.77
Reflection shellResolution: 3.293→3.41 Å / Num. measured obs: 7109 / Num. unique obs: 1639 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 3.29→19.85 Å / SU ML: 0.4714 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.9938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3167 3164 10.06 %
Rwork0.297 28293 -
obs0.2989 31457 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133.47 Å2
Refinement stepCycle: LAST / Resolution: 3.29→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 325 0 4880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344982
X-RAY DIFFRACTIONf_angle_d0.77146788
X-RAY DIFFRACTIONf_chiral_restr0.0487810
X-RAY DIFFRACTIONf_plane_restr0.005874
X-RAY DIFFRACTIONf_dihedral_angle_d9.5644696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.340.49091300.4091153X-RAY DIFFRACTION93.92
3.34-3.390.38511320.38481253X-RAY DIFFRACTION98.44
3.39-3.450.37031350.36061224X-RAY DIFFRACTION99.2
3.45-3.510.37321430.34441229X-RAY DIFFRACTION99.35
3.51-3.570.32181410.3421251X-RAY DIFFRACTION99.64
3.57-3.640.38871320.34651218X-RAY DIFFRACTION99.34
3.64-3.710.31921360.34691238X-RAY DIFFRACTION99.85
3.71-3.790.36211400.31241251X-RAY DIFFRACTION99.71
3.79-3.880.261400.31931221X-RAY DIFFRACTION99.56
3.88-3.980.36451350.3071232X-RAY DIFFRACTION99.42
3.98-4.080.371400.31281233X-RAY DIFFRACTION99.71
4.08-4.20.31241350.2881262X-RAY DIFFRACTION99.29
4.2-4.340.36361400.2661227X-RAY DIFFRACTION99.35
4.34-4.490.27551360.26181226X-RAY DIFFRACTION99.34
4.49-4.670.3121390.2651245X-RAY DIFFRACTION99.5
4.67-4.880.27481420.27031206X-RAY DIFFRACTION99.63
4.88-5.130.32361360.28481242X-RAY DIFFRACTION99.64
5.13-5.450.34891440.28681241X-RAY DIFFRACTION99.43
5.45-5.860.24781380.30381233X-RAY DIFFRACTION98.85
5.86-6.430.25571360.33971218X-RAY DIFFRACTION98.76
6.43-7.320.36541370.33711232X-RAY DIFFRACTION99.06
7.32-9.070.27061340.27211237X-RAY DIFFRACTION99.35
9.08-19.850.31411430.26421221X-RAY DIFFRACTION98.34
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)
16.13074243123-1.85323863362-0.6930254051477.834175424821.257265520793.087706372740.1168001205260.407038723407-0.00738551766986-0.918187560087-0.1333000170960.296075146521-0.386566562946-0.1736465103630.02967292448390.8070349883410.097376993537-0.1355729161340.7122499927620.1298809095250.985536977612-165.638703392168.1137928653.68267438946
23.339234163681.50297257168-2.014929869062.885729410630.9412763885566.88310720727-0.0594368634910.9568020415253.13245530157-1.976078910690.0949349026151.21166233157-0.946015672779-0.641513693275-0.1916635518721.0613558761-0.155923313034-0.1745703113880.7743631456670.4302706303761.67973522796-161.173605248188.8536190125.79048479822
35.572057543-0.6776798986090.3357909042741.40152171563-2.938130252966.04124905202-0.22080244725-0.6687918523160.415859166692-0.2491344219650.4830916159350.73837770949-0.767922529801-0.911901908469-0.4687099975471.06643115930.29045657846-0.1743663681310.829771935607-0.1348409531481.51395347113-178.424436757177.34500864616.6788070631
43.56747502252-1.07984103380.04079569708730.5326104971260.9133100104913.86434927264-0.733368204316-0.05533205397451.70583313506-0.6185787615620.592543038984-0.506409966002-2.060428771911.16299523405-0.1797499144821.64015224317-0.1525471467090.1532346110170.334855528332-0.2098169056461.95091568688-160.642370666194.77374825319.5854913268
54.54175876533-6.26328368505-3.187720480868.581422306844.904726218599.07666075764-0.77924308023-1.42565753701-1.770827891380.4469459872920.9610762562253.328337250540.0845392931842-0.338614196595-0.05010790185670.9313114774520.3202601100470.1176968330060.9582314645120.06331585865171.49138378476-167.646900636185.26351856531.480131598
64.17318077726-1.05234187676-2.007712556191.97516599304-4.964038235275.097167408950.249412679798-0.9969066340910.4284757429361.269124449041.091736078261.69623459565-1.4842994405-1.125442569540.6999476754040.9068628393890.47785385019-0.2719170102040.862163216436-0.6841073126830.337991052458-166.329900024184.97846936439.6154991089
74.970955827361.224818679681.544326710026.272681769863.93333027516.47191996879-0.4483860239160.186279247328-1.03777465837-0.1562529182120.6406912942422.69777918727-0.08969192228080.149520983247-0.08212681119470.8624664708540.4949928739820.09844233157011.151125642590.1486740641.13510229544-180.429789253157.5446082426.0326974703
82.91672225998-4.149268236224.385265640227.34711599506-7.791185573498.445306719170.320369086878-0.6340365034861.584273955030.303568385144-2.23144485298-4.78201099520.843910657681.911353612371.80404893841.403796974460.346947966750.3880917789721.985282265630.4974377843832.72198540582-165.123664638152.47407455339.1239459355
95.08698606286-3.48095901573-2.198659096857.918918587184.742449804898.16055758117-0.678792193118-0.563764369769-1.148635194380.8160242753580.6359169679980.742254232480.5025737062680.2158352674280.03765674467190.6938834133990.03173060013450.2198697413131.048027294730.2176281002071.33335118973-167.186486198145.76547850321.4870716742
103.95680513795-2.20032324176-1.602996401775.43595682602-1.847026339592.561572094610.2034680327510.2441949119220.097303392434-1.413782823280.06838057398952.322213898910.585315189581-0.80477536237-0.2876047926791.09292989722-0.118586388751-0.3447899960941.040519048490.006832976742621.69666402667-167.793789571137.4597310431.27639872346
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'R' and (resid 2 through 261 )RA2 - 2611 - 230
22chain 'R' and (resid 262 through 308 )RA262 - 308231 - 268
33chain 'R' and (resid 309 through 362 )RA309 - 362269 - 322
44chain 'R' and (resid 363 through 390 )RA363 - 390323 - 347
55chain 'R' and (resid 391 through 491 )RA391 - 491348 - 380
66chain 'R' and (resid 492 through 518 )RA492 - 518381 - 407
77chain 'Q' and (resid 102 through 119 )QB102 - 1191 - 18
88chain 'Q' and (resid 120 through 131 )QB120 - 13119 - 30
99chain 'Q' and (resid 132 through 216 )QB132 - 21631 - 117
1010chain 'Q' and (resid 217 through 294 )QB217 - 294118 - 195

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