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- PDB-8r67: tubulin-cryptophycin complex -

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Basic information

Entry
Database: PDB / ID: 8r67
Titletubulin-cryptophycin complex
Components
  • Detyrosinated tubulin alpha-1B chain
  • Stathmin-4
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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-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-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
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / : / Tubulin--tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsAbel, A.C. / Muehlethaler, T. / Dessin, C. / Steinmetz, M.O. / Sewald, N. / Prota, A.E.
Funding supportEuropean Union, Switzerland, 3items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860070European Union
Swiss National Science Foundation310030_192566 Switzerland
H2020 Marie Curie Actions of the European Commission642004European Union
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Bridging the maytansine and vinca sites: Cryptophycins target beta-tubulin's T5-loop.
Authors: Abel, A.C. / Muhlethaler, T. / Dessin, C. / Schachtsiek, T. / Sammet, B. / Sharpe, T. / Steinmetz, M.O. / Sewald, N. / Prota, A.E.
History
DepositionNov 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Detyrosinated tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Detyrosinated 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)266,32629
Polymers261,6316
Non-polymers4,69523
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, A,B,C,D,E,F
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24020 Å2
ΔGint-142 kcal/mol
Surface area80070 Å2
Unit cell
Length a, b, c (Å)104.750, 158.660, 180.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Detyrosinated tubulin alpha-1B chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / 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: A0A8V0Z8P0

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Non-polymers , 10 types, 577 molecules

#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.: 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-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
#9: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-Y74 / 2-[(3~{S},10~{R},13~{E},16~{S})-10-[(3-chloranyl-4-methoxy-phenyl)methyl]-6,6-dimethyl-2,5,9,12-tetrakis(oxidanylidene)-16-[(1~{S})-1-[(2~{R},3~{R})-3-phenyloxiran-2-yl]ethyl]-1,4-dioxa-8,11-diazacyclohexadec-13-en-3-yl]ethanoic acid


Mass: 671.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H39ClN2O10 / Feature type: SUBJECT OF INVESTIGATION
#13: 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
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5% PEG 4K, 8% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000022 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000022 Å / Relative weight: 1
ReflectionResolution: 2.2→49.52 Å / Num. obs: 152380 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 52.92 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09303 / Rpim(I) all: 0.02607 / Rrim(I) all: 0.09666 / Net I/σ(I): 20.5
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 13 % / Rmerge(I) obs: 2.611 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 15014 / CC1/2: 0.502 / Rpim(I) all: 0.7508 / Rrim(I) all: 2.718 / % possible all: 99.41

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→49.52 Å / SU ML: 0.288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 7620 5 %
Rwork0.1936 144740 -
obs0.1953 152362 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17302 0 297 554 18153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002418163
X-RAY DIFFRACTIONf_angle_d0.536524652
X-RAY DIFFRACTIONf_chiral_restr0.04152675
X-RAY DIFFRACTIONf_plane_restr0.00393203
X-RAY DIFFRACTIONf_dihedral_angle_d12.80486727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.37522400.36574552X-RAY DIFFRACTION95.02
2.22-2.250.38522510.34814758X-RAY DIFFRACTION99.88
2.25-2.280.3552530.32624813X-RAY DIFFRACTION99.96
2.28-2.310.35522490.30344729X-RAY DIFFRACTION99.92
2.31-2.340.32542540.28674812X-RAY DIFFRACTION99.92
2.34-2.370.31552530.27964798X-RAY DIFFRACTION99.9
2.37-2.40.30482530.27094810X-RAY DIFFRACTION99.92
2.4-2.440.28552500.25764767X-RAY DIFFRACTION99.96
2.44-2.480.26562520.24354784X-RAY DIFFRACTION99.96
2.48-2.520.31332520.2394794X-RAY DIFFRACTION99.98
2.52-2.560.25662520.2334787X-RAY DIFFRACTION100
2.56-2.610.25892540.21934827X-RAY DIFFRACTION100
2.61-2.660.3052510.22434762X-RAY DIFFRACTION99.98
2.66-2.710.27022530.22714817X-RAY DIFFRACTION99.96
2.71-2.770.29842540.22824812X-RAY DIFFRACTION99.9
2.77-2.830.28162530.22574807X-RAY DIFFRACTION99.92
2.83-2.910.26482530.22694808X-RAY DIFFRACTION100
2.91-2.980.27892540.22924823X-RAY DIFFRACTION100
2.98-3.070.24092540.21194822X-RAY DIFFRACTION100
3.07-3.170.25842540.20634834X-RAY DIFFRACTION99.98
3.17-3.280.23322540.20784827X-RAY DIFFRACTION99.98
3.28-3.420.25672540.19944833X-RAY DIFFRACTION99.98
3.42-3.570.23982540.19864811X-RAY DIFFRACTION100
3.57-3.760.22212570.18424881X-RAY DIFFRACTION100
3.76-40.19622560.16834866X-RAY DIFFRACTION99.98
4-4.30.18352560.16224879X-RAY DIFFRACTION100
4.3-4.740.16832580.14474886X-RAY DIFFRACTION100
4.74-5.420.20132590.15644923X-RAY DIFFRACTION100
5.42-6.830.23462610.18834957X-RAY DIFFRACTION100
6.83-49.520.18822720.17245161X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: 17.3903000541 Å / Origin y: 44.1668203398 Å / Origin z: 25.9949882465 Å
111213212223313233
T0.410307120411 Å20.0262824270622 Å20.0295909238699 Å2-0.519737098563 Å2-0.053590810944 Å2--0.576019769151 Å2
L0.174148653549 °2-0.0046438154242 °2-0.0720738561746 °2-0.698172192459 °20.66125738388 °2--1.1664579225 °2
S-0.0345805864745 Å °0.00702931767081 Å °-0.00477320851347 Å °0.0938201481376 Å °0.0702590500454 Å °-0.0125589224525 Å °0.0886616961862 Å °0.0627345049577 Å °-0.00106069433869 Å °
Refinement TLS groupSelection details: all

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