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- PDB-5nw5: Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from S... -

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Basic information

Entry
Database: PDB / ID: 5nw5
TitleCrystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA
Components
  • DNA (30-MER)
  • DNA (60-MER)
  • Telomere length regulator protein RIF1
KeywordsDNA BINDING 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
DNA / DNA (> 10) / Telomere length regulator protein RIF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.502 Å
AuthorsBunker, R.D. / Reinert, J.K. / 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 5, 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 / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 17, 2024Group: 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: Telomere length regulator protein RIF1
B: Telomere length regulator protein RIF1
C: DNA (60-MER)
D: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)299,9954
Polymers299,9954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, The dimeric assembly of RIF1-NTD with DNA assigned to the ASU is supported negative-stain electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-24 kcal/mol
Surface area117060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.140, 169.800, 390.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 140781.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: RIF1, YBR275C, YBR1743 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29539
#2: DNA chain DNA (60-MER)


Mass: 9351.247 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Directionality and sequence register of the DNA could not be established unequivocally. DNA duplex modeled as poly-T in the most plausible orientation. Chain C construct sequence: ...Details: Directionality and sequence register of the DNA could not be established unequivocally. DNA duplex modeled as poly-T in the most plausible orientation. Chain C construct sequence: ACGCTGCCGAATTCTACCAGTGCCTTGCTAGGACATCTTTGCCCACCTGCAGGTTCACCC.
Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (30-MER)


Mass: 9080.827 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Directionality and sequence register of the DNA could not be established unequivocally. DNA duplex modeled as poly-T in most plausible orientation. Chain D construct sequence: TAGCAAGGCACTGGTAGAATTCGGCAGCGT.
Source: (synth.) synthetic construct (others)

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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: 5.09 Å3/Da / Density % sol: 75.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: CRYSTAL GROWN BY DEHYDRATING 1 uL of PROTEIN-DNA MIXTURE (43.5 uM protein with 65 uM DNA) IN 50 mM HEPES PH 7.4, 310 mM NaCl, 1 mM TCEP over a reservoir containing 10 mM NiCl2, 100 mM Tris- ...Details: CRYSTAL GROWN BY DEHYDRATING 1 uL of PROTEIN-DNA MIXTURE (43.5 uM protein with 65 uM DNA) IN 50 mM HEPES PH 7.4, 310 mM NaCl, 1 mM TCEP over a reservoir containing 10 mM NiCl2, 100 mM Tris-HCl, pH 8, 20% (w/v) polyethylene glycol MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91863 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91863 Å / Relative weight: 1
ReflectionResolution: 6.5→43.25 Å / Num. obs: 12703 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 388 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.342 / Rpim(I) all: 0.102 / Net I/σ(I): 8
Reflection shellResolution: 6.5→7.27 Å / Redundancy: 12.5 % / Rmerge(I) obs: 6.011 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3529 / CC1/2: 0.142 / Rpim(I) all: 1.757 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2205: AMBER)refinement
XDSOct 15, 2015data reduction
Aimless0.5.23data scaling
PHASER2.7.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NVR

5nvr


Resolution: 6.502→43.232 Å / SU ML: 1.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.41
Details: ANISOTROPICALLY TRUNCATED STRUCTURE FACTOR AMPLITUDES GENERATED BY STARANISO USED FOR REFINEMENT. FINAL REFINEMENT CARRIED OUT WITH HYBRID PHENIX/AMBER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 578 6.51 %RANDOM SELECTION
Rwork0.2527 ---
obs0.2543 8877 70.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 331 Å2
Refinement stepCycle: LAST / Resolution: 6.502→43.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17640 1224 0 0 18864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01519362
X-RAY DIFFRACTIONf_angle_d2.11526471
X-RAY DIFFRACTIONf_dihedral_angle_d23.2217383
X-RAY DIFFRACTIONf_chiral_restr0.1083094
X-RAY DIFFRACTIONf_plane_restr0.0173109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5023-7.1540.4208590.3964650X-RAY DIFFRACTION23
7.154-8.18310.39761200.33481878X-RAY DIFFRACTION65
8.1831-10.28680.27421830.24982699X-RAY DIFFRACTION91
10.2868-43.23270.24312160.22863072X-RAY DIFFRACTION100

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