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- PDB-8ahm: Crystal structure of tubulin in complex with C(13)/C(13')-Bis-Des... -

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Basic information

Entry
Database: PDB / ID: 8ahm
TitleCrystal structure of tubulin in complex with C(13)/C(13')-Bis-Desmethyl-Disorazole Z
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / tubulin / 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 / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / 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 / spindle microtubule / 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 / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / 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 / Chem-M5U / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å
AuthorsOliva, M.A. / Diaz, J.F. / Altmann, K.H.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-104545RB-I00 Spain
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Synthesis and Biological Evaluation of C(13)/C(13')-Bis(desmethyl)disorazole Z.
Authors: Bold, C.P. / Lucena-Agell, D. / Oliva, M.A. / Diaz, J.F. / Altmann, K.H.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Feb 7, 2024Group: 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)270,99026
Polymers266,9126
Non-polymers4,07720
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.047, 157.800, 181.894
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: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / 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) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 22125.301 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 BL21(DE3) (bacteria) / 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 BL21(DE3) (bacteria) / References: UniProt: E1BQ43

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Non-polymers , 10 types, 189 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: 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
#11: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#12: Chemical ChemComp-M5U / dimethyl 2,2'-((12Z,122Z,4S,6Z,8E,10E,15S,17Z,19E,21E)-2,13-dioxo-3,14-dioxa-1(4,2),12(2,4)-dioxazolacyclodocosaphane-6,8,10,17,19,21-hexaene-4,15-diyl)(2S,2'S,3S,3'S,4E,4'E)-bis(3-hydroxyhex-4-enoate) / methyl (E,2S,3S)-2-[(4S,6Z,8E,10E,18S,20Z,22E,24E)-18-[(E,2S,3S)-1-methoxy-3-oxidanyl-1-oxidanylidene-hex-4-en-2-yl]-2,16-bis(oxidanylidene)-3,13,17,27-tetraoxa-29,30-diazatricyclo[24.2.1.1^{12,15}]triaconta-1(28),6,8,10,12(30),14,20,22,24,26(29)-decaen-4-yl]-3-oxidanyl-hex-4-enoate


Mass: 718.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H42N2O12 / 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.: 169 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES/0.1 M Imidazole pH 6.5, 0.03 M CaCl2/ MgCl2, 5 mM L-Tyr, 8% glycerol, 5.5 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918498465 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918498465 Å / Relative weight: 1
ReflectionResolution: 2.42→49.84 Å / Num. obs: 115614 / % possible obs: 99.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 54.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.032 / Rrim(I) all: 0.098 / Net I/σ(I): 14.4 / Num. measured all: 1023152 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.42-2.468.51.2514678055080.6680.4511.3321.696.4
13.25-49.847.90.03361887860.9990.0130.03644.998

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o2b

4o2b


Resolution: 2.42→49.84 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 5706 4.94 %
Rwork0.1999 109814 -
obs0.2019 115520 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.53 Å2 / Biso mean: 66.1763 Å2 / Biso min: 26.52 Å2
Refinement stepCycle: final / Resolution: 2.42→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17076 0 390 169 17635
Biso mean--70.47 48.66 -
Num. residues----2158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.450.41261860.38153430361695
2.45-2.480.41792000.332836223822100
2.48-2.510.37742030.321536073810100
2.51-2.540.30672000.292736023802100
2.54-2.570.29311910.283836283819100
2.57-2.610.32111750.268136253800100
2.61-2.640.30962230.259436153838100
2.64-2.680.28211880.255836503838100
2.68-2.720.31691940.249336223816100
2.72-2.770.27871850.251236633848100
2.77-2.820.30642040.250136013805100
2.82-2.870.31591880.258436453833100
2.87-2.920.30621860.267436473833100
2.92-2.980.31441710.270636773848100
2.98-3.050.30731930.242836283821100
3.05-3.120.30061710.247636483819100
3.12-3.20.28711860.238736803866100
3.2-3.280.26031730.236236903863100
3.28-3.380.25261990.224436073806100
3.38-3.490.25771930.218536553848100
3.49-3.610.26821830.214336853868100
3.61-3.760.25242010.196736863887100
3.76-3.930.22151710.171836703841100
3.93-4.140.18751910.159636783869100
4.14-4.40.15971830.149837073890100
4.4-4.730.17861770.135537183895100
4.73-5.210.19971650.145637283893100
5.21-5.960.21092010.17937443945100
5.96-7.510.2332040.189437923996100
7.51-49.840.20462210.17413864408599
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)
10.5666-0.3466-0.17460.20860.01350.19720.06390.038-0.1202-0.21020.1088-0.0422-0.3570.18180.0490.6526-0.13320.13420.4091-0.10940.395229.370897.668654.0185
20.3246-0.20280.10090.26360.18370.6028-0.07880.299-0.22-0.270.3331-0.1582-0.38530.41150.0550.5242-0.16770.14620.4853-0.12750.424734.306984.665545.1737
30.0341-0.0596-0.13530.32860.30220.19090.0417-0.0214-0.07150.0610.1807-0.0501-0.00330.25250.00570.3881-0.0540.03650.4957-0.18320.530433.058477.558257.9698
40.2486-0.0888-0.04060.20410.24530.61210.04590.0074-0.04570.13240.04920.0417-0.13370.1109-00.40240.00560.0330.3958-0.08070.4321.373584.768564.9127
50.18710.07850.06120.04050.0410.04280.1728-0.0891-0.03730.2417-0.1460.2109-0.07060.0062-00.55010.02870.10580.4699-0.10020.54589.204984.836571.7385
60.20560.14570.12140.69050.48760.76210.0283-0.0026-0.03630.337-0.00350.05840.04790.099500.48420.01970.02350.4126-0.09450.412223.024477.250969.8659
70.22020.0387-0.17210.042-0.03040.1768-0.0038-0.0224-0.0089-0.08080.01830.1046-0.1522-0.0879-00.43370.0606-0.00030.3364-0.06570.436815.087572.031222.7846
80.1462-0.01150.09350.0050.02640.18670.02640.46340.0054-0.2379-0.0412-0.0081-0.2825-0.1377-00.55530.05060.01390.56250.00750.483619.32767.094412.3342
90.3908-0.1569-0.01260.72350.65880.95630.04380.04360.0403-0.029-0.06580.0197-0.0740.0223-00.295-0.00510.01610.4048-0.08660.421419.860355.8325.6899
100.57780.09910.1310.3180.25740.6186-0.0489-0.04170.02260.0388-0.15840.0542-0.0247-0.2691-0.02570.34640.06540.01760.4637-0.14870.41166.271560.735442.5616
110.1477-0.23180.2730.10150.04230.28130.093-0.0146-0.01170.0634-0.22840.27710.1809-0.130200.4103-0.00820.03720.4167-0.07350.454314.455243.730634.1418
120.02230.0755-0.09150.2117-0.08280.0844-0.04370.0457-0.09210.25290.032-0.10820.12960.1105-00.41630.0073-0.01460.4447-0.04230.392425.253638.621231.5997
130.21820.10540.13050.51750.04780.4191-0.0470.0560.0109-0.03570.0597-0.0039-0.03330.003100.3154-0.03970.0170.37-0.01870.365216.760732.4669-9.8854
140.4498-0.17550.0290.39220.63630.5602-0.05920.00070.03830.0593-0.03990.01140.1219-0.1056-0.00010.3196-0.02270.02940.3195-0.03850.36987.861224.69625.4502
150.2477-0.0008-0.07680.2707-0.23570.1959-0.22540.51520.0641-0.24740.2929-0.00560.1215-0.19280.17110.6096-0.15270.00920.8125-0.07870.38116.83549.0252-44.058
160.53120.2413-0.38530.4618-0.10520.8034-0.15220.24590.0528-0.16910.0895-0.08050.19230.0182-0.02020.571-0.07640.09410.5551-0.16190.410222.836-2.6509-34.2247
170.3354-0.211-0.16480.10990.20080.7561-0.19870.2088-0.1074-0.05910.09150.04860.2773-0.18320.00020.568-0.06490.08610.468-0.1260.46113.3925-7.0346-22.3085
180.46570.13240.03080.03690.06420.0009-0.15320.17760.38220.55940.1136-0.2062-0.01280.02260.00650.9031-0.1159-0.00040.5631-0.12250.574127.780892.692282.3304
190.5126-0.0386-0.20080.10770.47170.1697-0.105-0.0467-0.00310.0727-0.04790.09910.19330.1928-0.48360.39720.04590.03470.4862-0.15680.407942.639728.4774.8586
200.23730.0129-0.33580.10360.13750.5574-0.19770.17240.0617-0.13570.0202-0.06390.4454-0.0101-0.00010.7169-0.07520.08570.4611-0.08460.53646.247455.10269.7101
210.10690.1055-0.07570.0771-0.08810.06380.10910.012-0.04950.0467-0.2061-0.275-0.5040.2332-00.642-0.0225-0.02860.7090.09290.630415.954664.3861100.5012
220.0330.13460.00320.42530.02850.00340.1795-0.1623-0.15840.4161-0.25580.2441-0.091-0.0397-0.0230.63780.1011-0.19151.14830.41890.975819.18453.5356107.9507
230.33890.0633-0.33090.06390.04910.4039-0.43730.0681-0.22590.11230.0214-0.25170.2691-0.1157-0.02310.750.10930.18260.35570.10710.5641-1.718153.480896.8813
240.02440.0184-0.0097-0.00570.0022-0.0014-0.4501-0.0132-0.4087-0.1418-0.2876-0.2220.07040.3838-01.37230.17780.20880.57160.18121.014.165539.6955103.9538
250.04280.12250.01410.10.10570.3518-0.23570.0786-0.01450.10370.34820.03480.2009-0.0528-00.72950.02910.13510.42640.08680.5457-6.008257.222298.3085
260.48730.0462-0.37110.14290.15140.3864-0.17630.0942-0.06830.07130.168-0.04520.1918-0.1089-00.6963-0.02220.0820.4490.05330.5671-1.165258.434486.0821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )A1 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 128 )A73 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 199 )A129 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 273 )A200 - 273
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )A274 - 311
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 437 )A312 - 437
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 55 )B1 - 55
8X-RAY DIFFRACTION8chain 'B' and (resid 56 through 94 )B56 - 94
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 259 )B95 - 259
10X-RAY DIFFRACTION10chain 'B' and (resid 260 through 372 )B260 - 372
11X-RAY DIFFRACTION11chain 'B' and (resid 373 through 401 )B373 - 401
12X-RAY DIFFRACTION12chain 'B' and (resid 402 through 439 )B402 - 439
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 259 )C1 - 259
14X-RAY DIFFRACTION14chain 'C' and (resid 260 through 440 )C260 - 440
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 88 )D2 - 88
16X-RAY DIFFRACTION16chain 'D' and (resid 89 through 266 )D89 - 266
17X-RAY DIFFRACTION17chain 'D' and (resid 267 through 440 )D267 - 440
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 46 )E6 - 46
19X-RAY DIFFRACTION19chain 'E' and (resid 47 through 141 )E47 - 141
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 66 )F1 - 66
21X-RAY DIFFRACTION21chain 'F' and (resid 67 through 135 )F67 - 135
22X-RAY DIFFRACTION22chain 'F' and (resid 136 through 184 )F136 - 184
23X-RAY DIFFRACTION23chain 'F' and (resid 185 through 223 )F185 - 223
24X-RAY DIFFRACTION24chain 'F' and (resid 224 through 257 )F224 - 257
25X-RAY DIFFRACTION25chain 'F' and (resid 258 through 302 )F258 - 302
26X-RAY DIFFRACTION26chain 'F' and (resid 303 through 380 )F303 - 380

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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

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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

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