[English] 日本語
Yorodumi
- PDB-1nyh: Crystal Structure of the Coiled-coil Dimerization Motif of Sir4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nyh
TitleCrystal Structure of the Coiled-coil Dimerization Motif of Sir4
ComponentsRegulatory protein SIR4
KeywordsTranscription repressor / coiled-coil / Transcription regulation / Repressor
Function / homology
Function and homology information


establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / double-strand break repair via nonhomologous end joining / heterochromatin formation / double-stranded DNA binding ...establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / double-strand break repair via nonhomologous end joining / heterochromatin formation / double-stranded DNA binding / molecular adaptor activity / chromosome, telomeric region
Similarity search - Function
Single helix bin / Sir4, SID domain / Sir4 SID domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein SIR4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsChang, J.F. / Hall, B.E. / Tanny, J.C. / Moazed, D. / Filman, D. / Ellenberger, T.
CitationJournal: Structure / Year: 2003
Title: Structure of the Coiled-coil Dimerization Motif of Sir4 and Its Interaction With Sir3
Authors: Chang, J.F. / Hall, B.E. / Tanny, J.C. / Moazed, D. / Filman, D. / Ellenberger, T.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulatory protein SIR4


Theoretical massNumber of molelcules
Total (without water)18,6531
Polymers18,6531
Non-polymers00
Water00
1
A: Regulatory protein SIR4

A: Regulatory protein SIR4


Theoretical massNumber of molelcules
Total (without water)37,3062
Polymers37,3062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area3690 Å2
ΔGint-40 kcal/mol
Surface area11230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.640, 108.640, 74.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -y, -x, 1/6+z and a translation of +1 along a, b and c axes.

-
Components

#1: Protein Regulatory protein SIR4 / Silent information regulator 4


Mass: 18652.967 Da / Num. of mol.: 1
Fragment: Coiled-coil dimerization domain, residue 1198-1358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR4 / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11978

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, MES, MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
250 mMHEPES1droppH7.5
3350 mM1dropNaCl
45 mMdithiothreitol1drop
51 mMEDTA1drop
6100 mMMES1reservoirpH6.0
7200 mM1reservoirMgCl2
81 %PEG33501reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97827, 0.978423, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2001 / Details: toroidal mirror
RadiationMonochromator: Channel-Cut Si(111)Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978271
20.9784231
30.951
ReflectionResolution: 3.1→47.14 Å / Num. all: 5054 / Num. obs: 4796 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 33.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 9.2 / % possible all: 97.2
Reflection
*PLUS
% possible obs: 96.2 % / Num. measured all: 191300
Reflection shell
*PLUS
% possible obs: 97.2 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→47.14 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.833 / SU B: 14.439 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.425 / ESU R Free: 0.345
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28797 501 10.5 %RANDOM
Rwork0.27074 ---
all0.27254 5054 --
obs0.27254 4290 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.993 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å20 Å2
3----3.26 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms592 0 0 0 592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022596
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.985796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.448575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02422
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.2280
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.184 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 44
Rwork0.347 277
Refinement
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.184

+
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