[English] 日本語
Yorodumi
- PDB-4bjs: Crystal structure of the Rif1 C-terminal domain (Rif1-CTD) from S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bjs
TitleCrystal structure of the Rif1 C-terminal domain (Rif1-CTD) from Saccharomyces cerevisiae
Components(TELOMERE LENGTH REGULATOR PROTEIN RIF1) x 2
KeywordsCELL CYCLE / TELOMERE ASSOCIATED PROTEINS
Function / homology
Function and homology information


negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / DNA double-strand break processing / shelterin complex / telomere capping / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication initiation / negative regulation of DNA-templated DNA replication initiation ...negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / DNA double-strand break processing / shelterin complex / telomere capping / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication initiation / negative regulation of DNA-templated DNA replication initiation / telomere maintenance / chromosome, telomeric region / cell cycle / nucleus
Similarity search - Function
Helix Hairpins - #1760 / Telomere-associated protein Rif1, N-terminal / Rap1-interacting factor 1 N terminal / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Telomere length regulator protein RIF1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.94 Å
AuthorsBunker, R.D. / Shi, T. / Gut, H. / Scrima, A. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Rif1 and Rif2 Shape Telomere Funcation and Architecture Through Multivalent RAP1 Interactions
Authors: Shi, T. / Bunker, R.D. / Mattarocci, S. / Ribeyre, C. / Faty, M. / Gut, H. / Scrima, A. / Rass, U. / Rubin, S.M. / Shore, D. / Thoma, N.H.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Atomic model / Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TELOMERE LENGTH REGULATOR PROTEIN RIF1
B: TELOMERE LENGTH REGULATOR PROTEIN RIF1
C: TELOMERE LENGTH REGULATOR PROTEIN RIF1
D: TELOMERE LENGTH REGULATOR PROTEIN RIF1


Theoretical massNumber of molelcules
Total (without water)28,8794
Polymers28,8794
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-68.9 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.789, 34.842, 46.214
Angle α, β, γ (deg.)87.41, 79.89, 82.31
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein TELOMERE LENGTH REGULATOR PROTEIN RIF1 / RAP1-INTERACTING FACTOR 1 / RAP1 INTERACTING FACTOR 1


Mass: 7216.321 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN (RIF1-CTD, RESIDUES 1857-1916)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29539
#2: Protein TELOMERE LENGTH REGULATOR PROTEIN RIF1 / RAP1-INTERACTING FACTOR 1 / RAP1 INTERACTING FACTOR 1


Mass: 7230.347 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RIF1-CTD, RESIDUES 1857-1916)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29539
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG 3000, 200 MM NACL, 100 HEPES/NAOH PH 7.5. PROTEIN WAS TREATED WITH 0.003% TRYPSIN IMMEDIATELY PRIOR TO CRYSTALLIZATION.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→45.5 Å / Num. obs: 15001 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 17.66 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shellResolution: 1.94→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 73.6

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: 14-MER POLY-ALA IDEALIZED ALPHA-HELIX

Resolution: 1.94→17.26 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9174 / SU R Cruickshank DPI: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 751 5.01 %RANDOM
Rwork0.1708 ---
obs0.1721 14980 95.82 %-
Displacement parametersBiso mean: 21.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.9066 Å20.1192 Å21.0919 Å2
2--1.7468 Å2-0.3853 Å2
3----3.6534 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: LAST / Resolution: 1.94→17.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 0 186 1900
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073524HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.896338HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d993SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it3524HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion213SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4288SEMIHARMONIC4
LS refinement shellResolution: 1.94→2.07 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2368 97 3.95 %
Rwork0.1848 2359 -
all0.1872 2456 -
obs--95.82 %
Refinement TLS params.Method: refined / Origin x: 10.8206 Å / Origin y: 41.6249 Å / Origin z: 33.4246 Å
111213212223313233
T-0.0533 Å2-0.0494 Å2-0.0503 Å2--0.0457 Å20.0253 Å2---0.0232 Å2
L0.9687 °2-0.2359 °2-0.0651 °2-0.9152 °20.1375 °2--0.5929 °2
S0 Å °-0.0673 Å °-0.0109 Å °-0.0617 Å °0.0114 Å °0.0099 Å °-0.0027 Å °0 Å °-0.0114 Å °
Refinement TLS groupSelection details: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more