[English] 日本語
Yorodumi
- PDB-7e4z: Crystal structure of tubulin in complex with Maytansinol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e4z
TitleCrystal structure of tubulin in complex with Maytansinol
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / microtubule assembly inhibitors / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. ...Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-BKL / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Rattus norvegicus (Norway rat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsWang, Y. / Li, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81703553 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: C3 ester side chain plays a pivotal role in the antitumor activity of Maytansinoids.
Authors: Li, W. / Huang, M. / Li, Y. / Xia, A. / Tan, L. / Zhang, Z. / Wang, Y. / Yang, J.
History
DepositionFeb 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,36225
Polymers255,3766
Non-polymers3,98619
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Hetero 6-mer - A2B2C1D1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23520 Å2
ΔGint-142 kcal/mol
Surface area81000 Å2
Unit cell
Length a, b, c (Å)104.431, 156.635, 182.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48966.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 48391.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16282.527 Da / Num. of mol.: 1
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
#4: Protein Tubulin tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 9 types, 393 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / 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.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#11: Chemical ChemComp-BKL / (1R,2S,3S,5S,6S,16E,18E,20R,21S)-11-chloro-6,21-dihydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaene-8,23-dione


Mass: 565.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37ClN2O8 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2, 30 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.69→40 Å / Num. obs: 83413 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 45.03 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.037 / Rrim(I) all: 0.138 / Χ2: 0.616 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.7-2.813.90.72382120.9390.1990.750.462
2.8-2.9113.70.5482770.9620.150.560.47
2.91-3.0413.40.40782410.9760.1150.4230.488
3.04-3.212.60.29182480.9840.0850.3040.533
3.2-3.413.80.21382790.9910.0590.2210.585
3.4-3.6613.80.15482840.9950.0430.160.672
3.66-4.0313.30.11683550.9960.0330.1210.785
4.03-4.6213.30.08983500.9970.0250.0930.836
4.62-5.8113.50.07984380.9980.0220.0820.717
5.81-4012.50.05787290.9980.0170.060.606

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TV8

4tv8


Resolution: 2.69→38.285 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 4059 4.88 %
Rwork0.1923 79133 -
obs0.194 83192 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.23 Å2 / Biso mean: 49.62 Å2 / Biso min: 12.29 Å2
Refinement stepCycle: final / Resolution: 2.69→38.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17406 0 370 374 18150
Biso mean--62.15 37.68 -
Num. residues----2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218222
X-RAY DIFFRACTIONf_angle_d0.64624760
X-RAY DIFFRACTIONf_chiral_restr0.0282695
X-RAY DIFFRACTIONf_plane_restr0.0023208
X-RAY DIFFRACTIONf_dihedral_angle_d14.4476809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.69-2.72150.33991280.2612245091
2.7215-2.75470.29551500.25862705100
2.7547-2.78950.31511530.26322668100
2.7895-2.82620.25241440.2412711100
2.8262-2.86490.29951400.2442695100
2.8649-2.90590.2911460.2352728100
2.9059-2.94920.2471470.25112692100
2.9492-2.99530.26031500.23312710100
2.9953-3.04440.27681310.23292742100
3.0444-3.09680.24451440.24112688100
3.0968-3.15310.27661360.23342744100
3.1531-3.21380.2771370.23462701100
3.2138-3.27930.27351370.22292737100
3.2793-3.35060.27491260.22082731100
3.3506-3.42850.27561360.21082729100
3.4285-3.51420.26181440.2042716100
3.5142-3.60910.24591320.19292736100
3.6091-3.71520.25381310.18432736100
3.7152-3.8350.20531430.17532740100
3.835-3.9720.2251390.1732740100
3.972-4.13080.20491580.16762736100
4.1308-4.31860.20881270.16472748100
4.3186-4.54590.19061420.14952770100
4.5459-4.83020.16651260.14692767100
4.8302-5.20230.20411300.15962783100
5.2023-5.72430.22621540.17762774100
5.7243-6.5490.19681240.19092820100
6.549-8.23760.21111570.17892817100
8.2376-38.2850.15371470.1537281996

+
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