[English] 日本語
Yorodumi
- PDB-5we0: Structural Basis for Shelterin Bridge Assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5we0
TitleStructural Basis for Shelterin Bridge Assembly
Components
  • DNA-binding protein rap1
  • Protection of telomeres protein poz1
  • Protection of telomeres protein tpz1
KeywordsGENE REGULATION / Telomere / Shelterin / Cooperativity
Function / homology
Function and homology information


meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / telomere-telomerase complex assembly / mitotic telomere tethering at nuclear periphery / telomere cap complex / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / mitotic telomere maintenance via semi-conservative replication / telomere maintenance via telomere lengthening ...meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / telomere-telomerase complex assembly / mitotic telomere tethering at nuclear periphery / telomere cap complex / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / mitotic telomere maintenance via semi-conservative replication / telomere maintenance via telomere lengthening / shelterin complex / nuclear telomere cap complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere maintenance via telomerase / telomere organization / telomere maintenance / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol
Similarity search - Function
S. pombe DNA-binding protein Rap1, C-terminal / Rap1, DNA-binding domain / Rap1, DNA-binding / TE2IP/Rap1 / Adrenocortical dysplasia protein / BRCT domain profile. / BRCT domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Protection of telomeres protein poz1 / Protection of telomeres protein tpz1 / DNA-binding protein rap1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, J.-K. / Liu, J. / Hu, X. / Yu, C. / Roskamp, K. / Sankaran, B. / Huang, L. / Komives, E.-A. / Qiao, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098943 United States
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for Shelterin Bridge Assembly.
Authors: Kim, J.K. / Liu, J. / Hu, X. / Yu, C. / Roskamp, K. / Sankaran, B. / Huang, L. / Komives, E.A. / Qiao, F.
History
DepositionJul 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protection of telomeres protein poz1
B: Protection of telomeres protein tpz1
C: DNA-binding protein rap1
D: Protection of telomeres protein poz1
E: Protection of telomeres protein tpz1
F: DNA-binding protein rap1
G: Protection of telomeres protein poz1
H: Protection of telomeres protein tpz1
I: DNA-binding protein rap1
J: Protection of telomeres protein poz1
K: Protection of telomeres protein tpz1
L: DNA-binding protein rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,27516
Polymers148,01312
Non-polymers2624
Water5,711317
1
A: Protection of telomeres protein poz1
B: Protection of telomeres protein tpz1
C: DNA-binding protein rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0694
Polymers37,0033
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-72 kcal/mol
Surface area14060 Å2
MethodPISA
2
D: Protection of telomeres protein poz1
E: Protection of telomeres protein tpz1
F: DNA-binding protein rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0694
Polymers37,0033
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-70 kcal/mol
Surface area13890 Å2
MethodPISA
3
G: Protection of telomeres protein poz1
H: Protection of telomeres protein tpz1
I: DNA-binding protein rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0694
Polymers37,0033
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-69 kcal/mol
Surface area13920 Å2
MethodPISA
4
J: Protection of telomeres protein poz1
K: Protection of telomeres protein tpz1
L: DNA-binding protein rap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0694
Polymers37,0033
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-70 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.720, 82.010, 103.510
Angle α, β, γ (deg.)89.99, 89.98, 73.96
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Protection of telomeres protein poz1 / Pot1-associated protein poz1


Mass: 29695.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: poz1, SPAC19G12.13c / Production host: Escherichia coli (E. coli) / References: UniProt: O13852
#2: Protein/peptide
Protection of telomeres protein tpz1 / Meiotically up-regulated gene 169 protein


Mass: 3964.574 Da / Num. of mol.: 4 / Fragment: UNP residues 476-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpz1, mug169, SPAC6F6.16c, SPAC6F6.18c / Production host: Escherichia coli (E. coli) / References: UniProt: O14246
#3: Protein/peptide
DNA-binding protein rap1


Mass: 3343.561 Da / Num. of mol.: 4 / Fragment: UNP residues 467-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rap1, SPBC1778.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96TL7
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 21% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999996 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999996 Å / Relative weight: 1
ReflectionResolution: 2.3→62.71 Å / Num. obs: 77768 / % possible obs: 97.6 % / Redundancy: 2.3 % / Net I/σ(I): 5.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHENIX(1.11.1_2575: ???)phasing
Coot0.8model building
MOSFLM7.2.1data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→62.705 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1978 2.54 %
Rwork0.1986 --
obs0.1994 77753 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→62.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8863 0 4 317 9184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019044
X-RAY DIFFRACTIONf_angle_d1.12312117
X-RAY DIFFRACTIONf_dihedral_angle_d17.4375537
X-RAY DIFFRACTIONf_chiral_restr0.0611282
X-RAY DIFFRACTIONf_plane_restr0.0061533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.36861260.27445512X-RAY DIFFRACTION97
2.3575-2.42130.28841250.25165313X-RAY DIFFRACTION97
2.4213-2.49250.27651490.23995446X-RAY DIFFRACTION97
2.4925-2.5730.28971580.22415374X-RAY DIFFRACTION97
2.573-2.66490.26831420.22195359X-RAY DIFFRACTION97
2.6649-2.77160.21711400.21445438X-RAY DIFFRACTION98
2.7716-2.89780.26171560.21795386X-RAY DIFFRACTION98
2.8978-3.05050.24551340.21845387X-RAY DIFFRACTION97
3.0505-3.24170.20951460.20755424X-RAY DIFFRACTION98
3.2417-3.49190.31531320.20325439X-RAY DIFFRACTION98
3.4919-3.84330.1811410.18915444X-RAY DIFFRACTION98
3.8433-4.39930.17441530.16935470X-RAY DIFFRACTION99
4.3993-5.54210.21281350.16955472X-RAY DIFFRACTION99
5.5421-62.72850.20761410.18675311X-RAY DIFFRACTION96

+
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