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- PDB-7vmk: Crystal structure of tubulin with 3 -

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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 / 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. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / 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; / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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

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