[English] 日本語
Yorodumi
- PDB-6th4: Tubulin-inhibitor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6th4
TitleTubulin-inhibitor complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / cytoskeleton / cell division / intracellular transport / TRANSPORT PROTEIN / MICROTUBULE
Function / homology
Function and homology information


microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / neuron projection development / growth cone / neuron projection / Golgi apparatus / cytoplasm
Similarity search - Function
Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile.
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-N9B / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.121 Å
AuthorsVarela, P.F. / Gigant, B.
CitationJournal: Acs Omega / Year: 2022
Title: B-nor-methylene Colchicinoid PT-100 Selectively Induces Apoptosis in Multidrug-Resistant Human Cancer Cells via an Intrinsic Pathway in a Caspase-Independent Manner
Authors: Stein, A. / Hilken nee Thomopoulou, P. / Frias, C. / Hopff, S.M. / Varela, P. / Wilke, N. / Mariappan, A. / Neudorfl, J.M. / Fedorov, A.Y. / Gopalakrishnan, J. / Gigant, B. / Prokop, A. / Schmalz, H.G.
History
DepositionNov 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,48920
Polymers217,1555
Non-polymers3,33515
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20160 Å2
ΔGint-177 kcal/mol
Surface area66320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.124, 128.304, 252.718
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16745.975 Da / Num. of mol.: 1 / Mutation: C14A, F20W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043

-
Non-polymers , 6 types, 132 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-N9B / 1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one


Mass: 340.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20O5 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG, LiSO4, PIPES BUFFER, pH 6.80

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.12→126 Å / Num. obs: 62794 / % possible obs: 94 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 15.1
Reflection shellResolution: 2.12→2.42 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3141 / CC1/2: 0.627 / Rrim(I) all: 1.151

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMar 15, 2019data reduction
autoPROC1.05data scaling
STARANISO1.04data scaling
PHASER2.8.0phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RYC

3ryc


Resolution: 2.121→126 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 1.107 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.974 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 3166 -RANDOM
Rwork0.1922 ---
obs0.1939 62794 52 %-
Displacement parametersBiso mean: 66.58 Å2
Baniso -1Baniso -2Baniso -3
1-14.1028 Å20 Å20 Å2
2---9.6682 Å20 Å2
3----4.4346 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.121→126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14512 0 207 117 14836
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815121HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9320517HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5262SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2678HARMONIC5
X-RAY DIFFRACTIONt_it15121HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion1958SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12046SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion18.89
LS refinement shellResolution: 2.121→2.316 Å
RfactorNum. reflection% reflection
Rfree0.2751 56 -
Rwork0.2209 --
obs--4.54 %
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)
12.9566-0.9108-0.91044.57661.0982.69790.0081-0.06390.3144-0.0639-0.02290.21670.31440.21670.01480.07240.0454-0.0244-0.3484-0.1602-0.300710.003832.662674.855
21.8949-1.7050.05035.4280.75032.2260.12-0.403-0.0239-0.403-0.12970.3339-0.02390.33390.00970.11480.0220.0619-0.34950.0174-0.2992.51370.138591.6739
31.5553-0.7633-0.26773.280.81361.56180.0224-0.2451-0.0162-0.2451-0.02540.1441-0.01620.14410.00290.13550.05060.067-0.2459-0.0314-0.0679-12.5903109.16103.262
43.0782-1.02660.27573.00660.09932.2830.1981-0.3105-0.0554-0.3105-0.25540.2744-0.05540.27440.0574-0.08970.04050.0285-0.3227-0.0075-0.3299-32.9793143.28116.834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|503 A|602 - A|608 E|4 - E|64 }A1 - 440
2X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|503 A|602 - A|608 E|4 - E|64 }A501 - 503
3X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|503 A|602 - A|608 E|4 - E|64 }A602 - 608
4X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|503 A|602 - A|608 E|4 - E|64 }E4 - 64
5X-RAY DIFFRACTION2{ B|1 - B|441 B|501 - B|504 E|65 - E|89 }B1 - 441
6X-RAY DIFFRACTION2{ B|1 - B|441 B|501 - B|504 E|65 - E|89 }B501 - 504
7X-RAY DIFFRACTION2{ B|1 - B|441 B|501 - B|504 E|65 - E|89 }E65 - 89
8X-RAY DIFFRACTION3{ C|1 - C|441 C|501 - C|503 C|606 - C|614 E|90 - E|115 D|501 - D|501 }C1 - 441
9X-RAY DIFFRACTION3{ C|1 - C|441 C|501 - C|503 C|606 - C|614 E|90 - E|115 D|501 - D|501 }C501 - 503
10X-RAY DIFFRACTION3{ C|1 - C|441 C|501 - C|503 C|606 - C|614 E|90 - E|115 D|501 - D|501 }C606 - 614
11X-RAY DIFFRACTION3{ C|1 - C|441 C|501 - C|503 C|606 - C|614 E|90 - E|115 D|501 - D|501 }E90 - 115
12X-RAY DIFFRACTION3{ C|1 - C|441 C|501 - C|503 C|606 - C|614 E|90 - E|115 D|501 - D|501 }D501
13X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|441 D|502 - D|505 }E116 - 141
14X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|441 D|502 - D|505 }D1 - 441
15X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|441 D|502 - D|505 }D502 - 505

+
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