[English] 日本語
Yorodumi
- PDB-2qk1: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qk1
TitleStructural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1
ComponentsProtein STU2
KeywordsPROTEIN BINDING / stu2 / Stu2p / XMAP215 / Dis1 / TOG / ch-TOG / HEAT repeat / microtubule plus end / +TIP
Function / homology
Function and homology information


repair of mitotic kinetochore microtubule attachment defect / microtubule plus end polymerase / mitotic sister chromatid biorientation / establishment or maintenance of microtubule cytoskeleton polarity / microtubule plus-end binding / spindle pole body / microtubule polymerization / mitotic spindle organization / spindle microtubule / kinetochore ...repair of mitotic kinetochore microtubule attachment defect / microtubule plus end polymerase / mitotic sister chromatid biorientation / establishment or maintenance of microtubule cytoskeleton polarity / microtubule plus-end binding / spindle pole body / microtubule polymerization / mitotic spindle organization / spindle microtubule / kinetochore / spindle pole / cell cortex / microtubule binding
Similarity search - Function
: / Stu2, C-terminal segment / XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant ...: / Stu2, C-terminal segment / XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsSlep, K.C. / Vale, R.D.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170, and EB1.
Authors: Slep, K.C. / Vale, R.D.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein STU2


Theoretical massNumber of molelcules
Total (without water)28,8981
Polymers28,8981
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.441, 80.649, 97.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsStu2p is a homodimer formed through a C-terminal coiled coil dimerization domain not included in this construct. Two TOG domains are arrayed at the N-terminal region. This construct embodies TOG domain 2.

-
Components

#1: Protein Protein STU2 / Suppressor of tubulin 2


Mass: 28898.441 Da / Num. of mol.: 1 / Fragment: TOG domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STU2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P46675
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 27% PEG 4000, 100 mM Sodium citrate, 200 mM Ammonium acetate, Protein concentration 15 mg/ml, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97959, 0.97972, 1.01627, 1.12714
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979591
20.979721
31.016271
41.127141
Reflection

D res high: 2.1 Å / D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
119.2925820.0441.022441097.2
219.4944530.0431.012461498.1
322.1897440.0391.012408796.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.525093.410.0311.03
3.594.529810.0321.027
3.143.5999.310.0381.02
2.853.1499.410.0461.038
2.652.8599.810.0511.035
2.492.6599.910.0641.032
2.372.4999.910.0691.037
2.262.3799.810.0731.012
2.182.2695.810.0750.954
2.12.1887.410.0920.955
4.525098.620.0311.02
3.594.5299.820.0321.026
3.143.5910020.0390.971
2.853.1410020.0461.014
2.652.8510020.0511.025
2.492.6510020.0621.033
2.372.4910020.0681.045
2.262.3799.820.0721.007
2.182.269620.0740.955
2.12.1887.420.0890.96
4.525099.930.0291.045
3.594.5210030.030.989
3.143.5910030.0361.039
2.853.1410030.0420.974
2.652.8510030.0470.963
2.492.6510030.0591.014
2.372.4999.930.0581.027
2.262.3796.830.0661.041
2.182.2687.730.0651.013
2.12.1877.530.0780.999
ReflectionResolution: 1.7→50 Å / Num. obs: 25288 / % possible obs: 99 % / Rmerge(I) obs: 0.04 / Rsym value: 4 / Χ2: 1.015 / Net I/σ(I): 25.4
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 9.4 / Num. unique all: 2381 / Rsym value: 9.7 / Χ2: 0.965 / % possible all: 94.6

-
Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 1.7→500.01 Å / Delta phi final: 0.176 / FOM : 0.194 / Reflection: 46701

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 1.7→41.85 Å / FOM work R set: 0.898 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4577 9.6 %Random 10%
Rwork0.173 ---
obs-24965 97.6 %-
Solvent computationBsol: 54.849 Å2
Displacement parametersBiso mean: 17.219 Å2
Baniso -1Baniso -2Baniso -3
1--0.151 Å20 Å20 Å2
2--3.716 Å20 Å2
3----3.565 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 0 313 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1541.5
X-RAY DIFFRACTIONc_scbond_it2.5422
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.7-1.710.195390.183501540
1.71-1.720.197970.172742839
1.72-1.740.272870.202800887
1.74-1.750.273830.199824907
1.75-1.760.1911010.177823924
1.76-1.770.189780.163821899
1.77-1.790.209910.184815906
1.79-1.80.259910.178811902
1.8-1.820.232760.183833909
1.82-1.830.221880.176864952
1.83-1.850.18720.159828900
1.85-1.860.174970.164860957
1.86-1.880.208880.192854942
1.88-1.90.271760.204880956
1.9-1.910.2421020.155800902
1.91-1.930.18960.178853949
1.93-1.950.151080.164825933
1.95-1.970.1631050.153826931
1.97-1.990.1951040.166853957
1.99-2.020.199910.172877968
2.02-2.040.234740.177901975
2.04-2.060.212920.166830922
2.06-2.090.1671060.154839945
2.09-2.110.177860.163849935
2.11-2.140.1961030.172880983
2.14-2.170.2051240.152856980
2.17-2.20.247800.169856936
2.2-2.240.2311040.166828932
2.24-2.270.22810.191885966
2.27-2.310.2021020.173865967
2.31-2.350.138750.149881956
2.35-2.390.197910.17875966
2.39-2.440.191780.179852930
2.44-2.490.1971060.173835941
2.49-2.540.172830.181907990
2.54-2.60.216750.191897972
2.6-2.660.218950.191823918
2.66-2.740.205880.183865953
2.74-2.820.1991160.176866982
2.82-2.910.271880.19862950
2.91-3.010.161030.172833936
3.01-3.130.215900.189884974
3.13-3.270.1991100.172836946
3.27-3.450.16810.165880961
3.45-3.660.1941290.164838967
3.66-3.950.184720.155881953
3.95-4.340.178890.164857946
4.34-4.970.1591000.157857957
4.97-6.260.197980.199854952
6.26-500.010.178880.182862950
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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