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- PDB-5nvr: Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from S... -

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Basic information

Entry
Database: PDB / ID: 5nvr
TitleCrystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae
ComponentsTelomere length regulator protein RIF1
KeywordsSTRUCTURAL PROTEIN / telomere maintenance / DNA double-strand break repair / irregular helical repeat / all-alpha fold
Function / homology
Function and homology information


negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / shelterin complex / centromeric DNA binding / telomere capping / DNA double-strand break processing / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication origin binding ...negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / shelterin complex / centromeric DNA binding / telomere capping / DNA double-strand break processing / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication origin binding / DNA replication initiation / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of DNA-templated DNA replication initiation / telomere maintenance / chromosome, telomeric region / nucleus
Similarity search - Function
Telomere-associated protein Rif1, N-terminal / Rap1-interacting factor 1 N terminal
Similarity search - Domain/homology
Telomere length regulator protein RIF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.95 Å
AuthorsBunker, R.D. / Shi, T. / Thoma, N.H.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends.
Authors: Mattarocci, S. / Reinert, J.K. / Bunker, R.D. / Fontana, G.A. / Shi, T. / Klein, D. / Cavadini, S. / Faty, M. / Shyian, M. / Hafner, L. / Shore, D. / Thoma, N.H. / Rass, U.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Telomere length regulator protein RIF1


Theoretical massNumber of molelcules
Total (without water)129,0541
Polymers129,0541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, SUPPORTED BY NEGATIVE STAIN ELECTRON MICROSCOPY
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area52910 Å2
2
A: Telomere length regulator protein RIF1

A: Telomere length regulator protein RIF1


Theoretical massNumber of molelcules
Total (without water)258,1082
Polymers258,1082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4150 Å2
ΔGint-18 kcal/mol
Surface area101670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.568, 203.568, 197.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Telomere length regulator protein RIF1 / RAP1-interacting factor 1


Mass: 129054.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RIF1, YBR275C, YBR1743 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29539
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: 4.62 Å3/Da / Density % sol: 73.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.8 mg/ml protein solution in 50 mM HEPES pH 7.4, 310 mM NaCl, 1 mM TCEP mixed equally (1 uL + 1 uL) with 100 mM Tris-HCl, pH 7.5, 320 mM lithium sulfate, 850 mM potassium sodium tartrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97902 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 22, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 3.94→49.43 Å / Num. obs: 21894 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 50.6 % / Biso Wilson estimate: 183 Å2 / Rmerge(I) obs: 0.234 / Net I/σ(I): 14.4
Reflection shellResolution: 3.94→4.16 Å / Redundancy: 42.7 % / Rmerge(I) obs: 4.131 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXDEV_2439refinement
DIALS1.0-predata reduction
Aimless0.5.26data scaling
SHARP2.8.1phasing
PHASER2.7.6phasing
RefinementMethod to determine structure: MAD / Resolution: 3.95→49.3 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 28.57
Details: ANOMALOUS PAIRS SEPARATED FOR REFINEMENT AND MLHL REFINEMENT TARGET USED WITH SE-SAD PHASE RESTRAINTS CALCULATED BY MR-SAD WITH PHASER. TLS ONLY ATOMIC DISPLACEMENT MODEL APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1132 5.18 %RANDOM SELECTION
Rwork0.212 ---
obs0.214 21828 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 221 Å2
Refinement stepCycle: LAST / Resolution: 3.95→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8691 0 0 0 8691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038862
X-RAY DIFFRACTIONf_angle_d0.54112002
X-RAY DIFFRACTIONf_dihedral_angle_d13.2023336
X-RAY DIFFRACTIONf_chiral_restr0.0431412
X-RAY DIFFRACTIONf_plane_restr0.0031502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9454-4.03720.3251520.32132512X-RAY DIFFRACTION98
4.0372-4.13810.33321420.31092535X-RAY DIFFRACTION100
4.1381-4.24990.3471530.29522565X-RAY DIFFRACTION100
4.2499-4.37490.3641400.27752539X-RAY DIFFRACTION100
4.3749-4.5160.39221180.26982587X-RAY DIFFRACTION100
4.516-4.67730.26731200.24312533X-RAY DIFFRACTION100
4.6773-4.86440.34451370.22372581X-RAY DIFFRACTION100
4.8644-5.08560.27551660.21882528X-RAY DIFFRACTION100
5.0856-5.35340.27081470.20992555X-RAY DIFFRACTION100
5.3534-5.68840.29461570.21342520X-RAY DIFFRACTION100
5.6884-6.12680.3531430.22512538X-RAY DIFFRACTION100
6.1268-6.7420.3471250.23752583X-RAY DIFFRACTION100
6.742-7.71440.26231080.20412561X-RAY DIFFRACTION100
7.7144-9.70710.17911300.14352573X-RAY DIFFRACTION100
9.7071-49.29980.20231520.19592524X-RAY DIFFRACTION99
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)
10.680.27360.50871.83820.4162.5218-0.4726-0.0892-0.0438-0.06120.1382-0.1084-0.47690.224-01.0751-0.1969-0.11960.9952-0.30061.324942.0854185.841476.1956
24.73651.43391.93641.49791.07391.5159-0.02120.4093-0.4853-0.2860.3269-0.2376-0.1090.1242-01.0287-0.00550.03561.0105-0.22580.966616.6818145.280642.6536
3-0.9061-0.88810.28091.36620.94421.50870.20450.1245-0.16980.48260.2465-0.39670.4185-0.12530.00261.226-0.3129-0.03251.5208-0.38561.1905-47.510584.2137-0.6675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 185 THROUGH 532 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 533 THROUGH 899 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 900 THROUGH 1256 )

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