[English] 日本語
Yorodumi
- PDB-4jqf: Structure of the C-terminal domain of human telomeric Stn1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jqf
TitleStructure of the C-terminal domain of human telomeric Stn1
ComponentsCST complex subunit STN1
KeywordsDNA BINDING PROTEIN / Wing-helix-turn-helix (wHTH) motif / Protein binding / Pol alpha / Ctc1
Function / homology
Function and homology information


CST complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / telomere capping / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / intermediate filament cytoskeleton / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance ...CST complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / telomere capping / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / intermediate filament cytoskeleton / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance / positive regulation of DNA replication / fibrillar center / single-stranded DNA binding / chromosome, telomeric region / intracellular membrane-bounded organelle / nucleoplasm / nucleus
Similarity search - Function
CST, Suppressor of Cdc13 homolog, complex subunit STN1, N-terminal domain / CST complex subunit Stn1 / Stn1, C-terminal / CST complex subunit Stn1, wHTH1 motif superfamily / CST, complex subunit STN1, C terminal / Replication factor A protein-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...CST, Suppressor of Cdc13 homolog, complex subunit STN1, N-terminal domain / CST complex subunit Stn1 / Stn1, C-terminal / CST complex subunit Stn1, wHTH1 motif superfamily / CST, complex subunit STN1, C terminal / Replication factor A protein-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CST complex subunit STN1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsBryan, C.F. / Rice, C.T. / Harkisheimer, M. / Schultz, D. / Skordalakes, E.
CitationJournal: Plos One / Year: 2013
Title: Structure of the human telomeric stn1-ten1 capping complex.
Authors: Bryan, C. / Rice, C. / Harkisheimer, M. / Schultz, D.C. / Skordalakes, E.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: CST complex subunit STN1


Theoretical massNumber of molelcules
Total (without water)20,4731
Polymers20,4731
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.805, 76.572, 114.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsheterotrimer

-
Components

#1: Protein CST complex subunit STN1 / Oligonucleotide/oligosaccharide-binding fold-containing protein 1 / Suppressor of cdc thirteen homolog


Mass: 20473.260 Da / Num. of mol.: 1 / Fragment: unp residues 191-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OBFC1, STN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H668
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 8.5
Details: 1.6 M Ammonium phosphate dibasic, 100 mM Tris, 3% Ethylene glycol, pH 8.5, VAPOR DIFFUSION, Microbatch Crystallization, temperature 289.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0076, 1.1000
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00761
21.11
ReflectionResolution: 1.6→20 Å / Num. all: 34343 / Num. obs: 34343 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.641 Å / Redundancy: 4 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.486 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.843 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21899 1718 5 %RANDOM
Rwork0.19744 ---
obs0.19852 32625 99.9 %-
all-32625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 0 166 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021374
X-RAY DIFFRACTIONr_angle_refined_deg0.9381.9661853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5065166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02125.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67915258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.883156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211019
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 116 -
Rwork0.333 2118 -
obs--99.33 %
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)
10.07750.2033-0.20571.0216-0.47740.57270.01480.00740.01280.1097-0.00020.0093-0.02320.0014-0.01460.01460.00350.0020.03220.02770.0317-2.104633.201393.9258
20.15150.3396-0.30230.9639-0.60470.63280.02890.0080.00850.0876-0.01630.0132-0.0575-0.0209-0.01260.01420.0080.00880.02210.02260.0326-2.50433.850890.8656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A190 - 368
2X-RAY DIFFRACTION2A401 - 566

+
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