[English] 日本語
Yorodumi
- PDB-4bj6: Crystal structure Rif2 in complex with the C-terminal domain of R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bj6
TitleCrystal structure Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)
Components
  • (RAP1-INTERACTING FACTOR 2) x 2
  • DNA-BINDING PROTEIN RAP1
KeywordsTRANSCRIPTION / GENOME STABILITY / TELOMERE ASSOCIATED PROTEINS / AAA+ FOLD
Function / homology
Function and homology information


positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding / telomere capping / regulation of glycolytic process / silent mating-type cassette heterochromatin formation / DNA binding, bending / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / telomere maintenance via telomerase / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / nucleosomal DNA binding / TBP-class protein binding / telomere maintenance / protein-DNA complex / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1650 / Rossmann fold - #12060 / : / : / RIF2, ASCE domain / RIF2, AAA+ lid domain / Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / Rap1, DNA-binding domain / TRF2-interacting telomeric protein/Rap1, C-terminal ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1650 / Rossmann fold - #12060 / : / : / RIF2, ASCE domain / RIF2, AAA+ lid domain / Arc Repressor Mutant, subunit A - #2170 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1480 / Rap1, DNA-binding domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein RAP1 / Protein RIF2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsShi, T. / Bunker, R.D. / 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 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAP1-INTERACTING FACTOR 2
B: RAP1-INTERACTING FACTOR 2
C: DNA-BINDING PROTEIN RAP1
D: RAP1-INTERACTING FACTOR 2
E: DNA-BINDING PROTEIN RAP1
F: RAP1-INTERACTING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,83816
Polymers133,8776
Non-polymers96110
Water00
1
B: RAP1-INTERACTING FACTOR 2
C: DNA-BINDING PROTEIN RAP1
D: RAP1-INTERACTING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4198
Polymers66,9393
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-94.5 kcal/mol
Surface area22300 Å2
MethodPISA
2
A: RAP1-INTERACTING FACTOR 2
E: DNA-BINDING PROTEIN RAP1
F: RAP1-INTERACTING FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4198
Polymers66,9393
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-95.4 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.250, 112.680, 140.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RAP1-INTERACTING FACTOR 2


Mass: 42145.809 Da / Num. of mol.: 2 / Fragment: N-TERMINALLY TRUNCATED, RESIDUES 35-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PAD DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q06208
#2: Protein DNA-BINDING PROTEIN RAP1 / REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN / SBF-E / TUF


Mass: 23248.975 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 627-827
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PAD DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P11938
#3: Protein/peptide RAP1-INTERACTING FACTOR 2


Mass: 1543.956 Da / Num. of mol.: 2
Fragment: RAP1 C-TERMINAL DOMAIN BINDING MODULE, RESIDUES 36-48
Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q06208
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 22-25% PEG 6000, 100 MM TRIS/HCL PH 8.0, 500 MM LI2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.26→48.8 Å / Num. obs: 27519 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 113.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.1
Reflection shellResolution: 3.26→3.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4BJ1 AND 3OWT

4bj1

3owt


Resolution: 3.26→48.79 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.322
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1361 4.96 %RANDOM
Rwork0.1719 ---
obs0.1731 27419 99.65 %-
Displacement parametersBiso mean: 110.75 Å2
Baniso -1Baniso -2Baniso -3
1-19.7177 Å20 Å20 Å2
2---30.0411 Å20 Å2
3---10.3234 Å2
Refine analyzeLuzzati coordinate error obs: 0.716 Å
Refinement stepCycle: LAST / Resolution: 3.26→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 50 0 7370
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017513HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1210169HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3505SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1052HARMONIC5
X-RAY DIFFRACTIONt_it7513HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion3.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1005SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8562SEMIHARMONIC4
LS refinement shellResolution: 3.26→3.38 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2324 120 4.25 %
Rwork0.2306 2704 -
all0.2307 2824 -
obs--99.65 %
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)
11.2073-1.4587-0.97764.5032.95563.18830.15020.0115-0.1011-0.2072-0.28750.21540.1522-0.16470.1373-0.04110.0010.07-0.19610.0181-0.1221-3.247-15.226730.3213
22.62671.73342.54992.92912.3296.09430.2042-0.07250.23810.1044-0.1187-0.22610.10340.1494-0.0855-0.2626-0.056-0.1061-0.27180.0671-0.126-30.62271.948112.0182
38.99761.3917-3.82541.7698-0.7195.2139-0.1778-0.56670.15860.25220.29780.46910.2261-0.0899-0.12-0.29330.023-0.0006-0.05110.1146-0.0742-54.78153.112832.8149
47.372.1427-0.70813.925-0.37012.0959-0.15530.18910.5432-0.1473-0.1216-0.39190.05380.6210.2769-0.20960.05220.1748-0.09920.1686-0.039621.03175.083931.0463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN E

+
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