[English] 日本語
Yorodumi
- PDB-7vmk: Crystal structure of tubulin with 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vmk
TitleCrystal structure of tubulin with 3
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / 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 / cellular response to interleukin-4 / tubulin binding / 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 / cellular response to interleukin-4 / tubulin binding / 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 / Helix hairpin bin / 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. ...Rossmann fold - #11480 / Helix hairpin bin / 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. / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-7PL / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / 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: 2.5 Å
AuthorsJifa, Z. / Lun, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of tubulin with 3
Authors: Jifa, Z. / Lun, T.
History
DepositionOct 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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-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)264,91023
Polymers261,3056
Non-polymers3,60517
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22920 Å2
ΔGint-109 kcal/mol
Surface area81440 Å2
Unit cell
Length a, b, c (Å)104.831, 157.513, 182.187
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: 50041.273 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: 49999.887 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: 16844.162 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, 182 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-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.: 4 / 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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical ChemComp-7PL / N-[3-[[6-[[3-(trifluoromethyl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide


Mass: 413.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F3N5O / 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.: 165 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 104668 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 37.52 Å2 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Rrim(I) all: 0.172 / Χ2: 0.968 / Net I/σ(I): 4 / Num. measured all: 1325667
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.549.81.36551610.6610.4421.4370.9399.8
2.54-2.5910.51.22751490.7180.3821.2870.93399.9
2.59-2.6411.21.17951620.770.3571.2340.94999.9
2.64-2.6911.81.17551780.790.351.2270.965100
2.69-2.7512.21.06452010.8330.3141.110.943100
2.75-2.8212.20.93851650.8590.2780.980.96699.9
2.82-2.8912.80.78651770.9080.2280.8190.993100
2.89-2.9613.70.69151810.9240.1930.7181.019100
2.96-3.0513.70.52752160.9580.1470.5470.988100
3.05-3.1513.50.4251950.9730.1180.4360.986100
3.15-3.2613.30.34251930.9810.0970.3560.996100
3.26-3.3912.70.26652330.9870.0770.2781.001100
3.39-3.5512.70.20352030.9930.0590.2121.046100
3.55-3.7313.80.16152320.9950.0450.1671.071100
3.73-3.9713.80.1252380.9970.0330.1251.067100
3.97-4.2713.60.09252580.9980.0260.0951.022100
4.27-4.712.60.0752630.9980.0210.0730.969100
4.7-5.3813.90.06853180.9990.0190.0710.929100
5.38-6.7812.90.07153720.9980.020.0740.856100
6.78-5012.50.0455730.9990.0120.0420.70299.9

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55

4i55


Resolution: 2.5→49.73 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1999 1.94 %
Rwork0.194 100905 -
obs0.1948 102904 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.7 Å2 / Biso mean: 48.1993 Å2 / Biso min: 12.02 Å2
Refinement stepCycle: final / Resolution: 2.5→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17424 0 220 165 17809
Biso mean--45.1 37.85 -
Num. residues----2199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.31661230.27146226634986
2.56-2.630.2711370.25276894703195
2.63-2.710.32651410.26037145728698
2.71-2.80.33031440.24097199734399
2.8-2.90.26661430.237272447387100
2.9-3.010.2721440.23372907434100
3.01-3.150.26131440.228572727416100
3.15-3.320.25681450.218672917436100
3.32-3.520.28131440.202772987442100
3.52-3.80.20721460.186473457491100
3.8-4.180.19691460.163273647510100
4.18-4.780.17171460.147373907536100
4.78-6.020.19331480.17174407588100
6.02-49.730.21751480.16747507765597

+
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