[English] 日本語
Yorodumi
- PDB-7s1t: Structure of the human POT1-TPP1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s1t
TitleStructure of the human POT1-TPP1 complex
Components
  • Adrenocortical dysplasia protein homolog
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN / POT1 / Telomere
Function / homology
Function and homology information


positive regulation of DNA strand elongation / positive regulation of telomeric D-loop disassembly / G-rich single-stranded DNA binding / telomere assembly / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere ...positive regulation of DNA strand elongation / positive regulation of telomeric D-loop disassembly / G-rich single-stranded DNA binding / telomere assembly / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere / DEAD/H-box RNA helicase binding / telomerase inhibitor activity / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / telomerase holoenzyme complex / Removal of the Flap Intermediate from the C-strand / embryonic limb morphogenesis / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / Telomere Extension By Telomerase / telomere maintenance via telomerase / Packaging Of Telomere Ends / DNA polymerase binding / positive regulation of telomere maintenance via telomerase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / skeletal system development / intracellular protein transport / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nuclear body / protein-containing complex binding / nucleoplasm
Similarity search - Function
: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 ...: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Adrenocortical dysplasia protein homolog / Protection of telomeres protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAramburu, T. / Skordalakes, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: POT1-TPP1 binding stabilizes POT1, promoting efficient telomere maintenance.
Authors: Aramburu, T. / Kelich, J. / Rice, C. / Skordalakes, E.
History
DepositionSep 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protection of telomeres protein 1
D: Protection of telomeres protein 1
G: Protection of telomeres protein 1
J: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
E: Adrenocortical dysplasia protein homolog
H: Adrenocortical dysplasia protein homolog
K: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,41312
Polymers181,1518
Non-polymers2624
Water00
1
A: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-39 kcal/mol
Surface area19100 Å2
MethodPISA
2
D: Protection of telomeres protein 1
E: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-38 kcal/mol
Surface area19170 Å2
MethodPISA
3
G: Protection of telomeres protein 1
H: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-38 kcal/mol
Surface area19120 Å2
MethodPISA
4
J: Protection of telomeres protein 1
K: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3533
Polymers45,2882
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-39 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.880, 70.980, 103.790
Angle α, β, γ (deg.)76.760, 84.610, 70.550
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Protection of telomeres protein 1 / hPot1 / POT1-like telomere end-binding protein


Mass: 35446.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9NUX5
#2: Protein
Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 9841.022 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, PIP1, PTOP, TINT1, TPP1 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q96AP0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5 and 3.0M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→36.44 Å / Num. obs: 36930 / % possible obs: 90 % / Redundancy: 5.9 % / CC1/2: 0.996 / Net I/σ(I): 9.32
Reflection shellResolution: 2.9→2.98 Å / Num. unique obs: 2747 / CC1/2: 0.55

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UN7

5un7


Resolution: 2.9→36.44 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 36.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3069 1845 5 %
Rwork0.2504 35078 -
obs0.2532 36923 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 276.88 Å2 / Biso mean: 76.1356 Å2 / Biso min: 27.36 Å2
Refinement stepCycle: final / Resolution: 2.9→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11776 0 4 0 11780
Biso mean--68.28 --
Num. residues----1504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.980.38761410.36892707284889
2.98-3.070.42031450.35572757290292
3.07-3.160.43161460.32672769291592
3.16-3.280.36681430.32782723286690
3.28-3.410.34171400.29922676281689
3.41-3.560.39751330.28462525265883
3.56-3.750.32321430.26422713285691
3.75-3.990.32051450.25332756290192
3.99-4.290.32221420.22612710285291
4.29-4.730.24921340.21352546268084
4.73-5.410.28231490.21342825297494
5.41-6.80.2811410.24232670281189
6.81-36.440.23961430.21212701284490

+
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