[English] 日本語
Yorodumi
- PDB-6cok: Structure of the 2nd TOG domain from yeast CLASP protein STU1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cok
TitleStructure of the 2nd TOG domain from yeast CLASP protein STU1
ComponentsProtein STU1
KeywordsPROTEIN BINDING / Heat repeat / single domain
Function / homology
Function and homology information


astral microtubule depolymerization / mitotic spindle midzone / attachment of spindle microtubules to kinetochore / kinetochore binding / polar microtubule / microtubule organizing center / cytoplasmic microtubule / beta-tubulin binding / mitotic spindle assembly / spindle microtubule ...astral microtubule depolymerization / mitotic spindle midzone / attachment of spindle microtubules to kinetochore / kinetochore binding / polar microtubule / microtubule organizing center / cytoplasmic microtubule / beta-tubulin binding / mitotic spindle assembly / spindle microtubule / mitotic spindle / kinetochore / microtubule binding / cell division / nucleus
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMajumdar, S. / Rice, L.M.
CitationJournal: Mol. Biol. Cell / Year: 2018
Title: An isolated CLASP TOG domain suppresses microtubule catastrophe and promotes rescue.
Authors: Majumdar, S. / Kim, T. / Chen, Z. / Munyoki, S. / Tso, S.C. / Brautigam, C.A. / Rice, L.M.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein STU1


Theoretical massNumber of molelcules
Total (without water)36,8611
Polymers36,8611
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.412, 111.009, 44.937
Angle α, β, γ (deg.)90.00, 101.36, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein STU1 / Suppressor of tubulin 1


Mass: 36861.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: STU1, YBL034C, YBL0416 / Production host: Escherichia coli (E. coli) / References: UniProt: P38198
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18% PEG3350, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 23899 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.04 / Net I/σ(I): 16.7
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.568 / Rpim(I) all: 0.33

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→40.949 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.2121 1152 5 %
Rwork0.1728 --
obs0.1747 23025 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→40.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 0 161 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072242
X-RAY DIFFRACTIONf_angle_d0.813043
X-RAY DIFFRACTIONf_dihedral_angle_d11.3471387
X-RAY DIFFRACTIONf_chiral_restr0.047367
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8885-1.97440.29291160.21412211X-RAY DIFFRACTION76
1.9744-2.07850.22791390.19162646X-RAY DIFFRACTION92
2.0785-2.20880.22991490.17782808X-RAY DIFFRACTION98
2.2088-2.37930.22211490.16912855X-RAY DIFFRACTION99
2.3793-2.61870.20631500.17352836X-RAY DIFFRACTION98
2.6187-2.99750.21941490.17812827X-RAY DIFFRACTION99
2.9975-3.77610.23531480.16892830X-RAY DIFFRACTION99
3.7761-40.9590.1691520.1612860X-RAY DIFFRACTION98
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)
12.87590.84151.56363.8951-1.34334.27630.29940.0558-0.159-0.2162-0.1956-0.55020.35440.32040.06570.10880.00840.04980.1977-0.04130.213115.771645.512245.6265
22.1487-0.0107-0.89851.9155-0.2680.8449-0.0520.4384-0.2994-0.32020.0140.0214-0.025-0.3667-0.06320.27890.0257-0.13520.1322-0.01960.22931.520418.653227.1715
32.26690.3185-0.90497.3246-5.4296.50020.09270.1147-0.1675-0.1655-0.0231-0.0504-0.00690.1306-0.04850.15020.005-0.02120.1205-0.07240.09992.071619.716332.1463
41.83110.4655-0.13027.2446-2.67494.73430.0726-0.0035-0.11060.26060.0909-0.2114-0.1059-0.0031-0.130.11290.03370.00160.0846-0.04130.10662.233724.431338.9047
52.27890.46180.45132.518-0.29184.4974-0.1525-0.187-0.06380.45760.0997-0.2907-0.1044-0.20910.04640.2360.0468-0.05340.1153-0.04520.16271.986632.040545.1864
62.68070.05770.03964.0947-0.66792.1652-0.01990.02240.1739-0.24490.02040.17610.0759-0.2964-0.00010.0718-0.0078-0.00010.1525-0.04560.1482-3.209442.031846.0409
72.05980.5273-0.52293.0603-0.55832.197-0.0001-0.04310.1096-0.0568-0.05940.1383-0.0475-0.05640.02120.0527-0.01780.01570.1627-0.05360.10682.091247.908749.6916
81.42520.06991.03633.9346-1.52523.3240.0843-0.30790.19120.4701-0.05260.0592-0.3623-0.0829-0.01060.1159-0.03480.03120.211-0.07240.13855.630453.784156.8674
96.9219-1.9361-1.57377.6461-0.17078.02260.3842-0.93140.42711.7285-0.1355-0.0484-0.3492-0.0579-0.15990.5918-0.25110.01820.616-0.1410.46188.93254.722862.8795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 273 )
8X-RAY DIFFRACTION8chain 'A' and (resid 274 through 301 )
9X-RAY DIFFRACTION9chain 'A' and (resid 302 through 319 )

+
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