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- PDB-4drx: GTP-Tubulin in complex with a DARPIN -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4drx
TitleGTP-Tubulin in complex with a DARPIN
Components
  • Designed ankyrin repeat protein (DARPIN) D1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / DARPin / SUBTILISIN / TUBULIN / TUBULIN DIGESTED WITH SUBTILISIN
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / adult locomotory behavior / intracellular protein transport / neuron migration / synapse organization / neuromuscular junction / visual learning / recycling endosome / structural constituent of cytoskeleton / cerebral cortex development / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / mitotic cell cycle / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciesARTIFICIAL GENE (others)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsPecqueur, L. / Gigant, B. / Knossow, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end.
Authors: Pecqueur, L. / Duellberg, C. / Dreier, B. / Jiang, Q. / Wang, C. / Pluckthun, A. / Surrey, T. / Gigant, B. / Knossow, M.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Designed ankyrin repeat protein (DARPIN) D1
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,40814
Polymers230,2186
Non-polymers2,1908
Water6,215345
1
A: Tubulin alpha chain
B: Tubulin beta chain
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2047
Polymers115,1093
Non-polymers1,0954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area36490 Å2
MethodPISA
2
C: Tubulin alpha chain
D: Tubulin beta chain
E: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2047
Polymers115,1093
Non-polymers1,0954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-20 kcal/mol
Surface area36350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.884, 90.596, 117.575
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and (resseq 1:42 or resseq 45: 54 or...
211chain 'D' and (resseq 1:42 or resseq 45: 54 or...
112chain 'A' and (resseq 2:37 or resseq 47: 279 or...
212chain 'C' and (resseq 2:37 or resseq 47: 279 or...
113chain 'E' and (resseq 13:167 ) and (not element H)
213chain 'F' and (resseq 13:167 ) and (not element H)

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha chain


Mass: 48665.027 Da / Num. of mol.: 2 / Fragment: UNP residues 1-437 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 48375.348 Da / Num. of mol.: 2 / Fragment: UNP residues 1-431 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein Designed ankyrin repeat protein (DARPIN) D1


Mass: 18068.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PDST067 (pQE30 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): XLIblue

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Non-polymers , 3 types, 353 molecules

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


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN ALPHA 1B ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN ALPHA 1B SEQUENCE (UNP81947) WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR BETA-TUBULIN (CHAIN B AND CHAIN D), THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN. THEY USED THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_ 999 001003900.1)

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 292 K / pH: 7
Details: PEG 6K, 0.05M KCl, 0.01 M MGCL2, 0.2M LiCl, 0.01 M HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.22→39.19 Å / Num. obs: 104776 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.98 % / Rmerge(I) obs: 0.015 / Net I/σ(I): 12.38
Reflection shellResolution: 2.22→2.35 Å / Mean I/σ(I) obs: 2.08 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RYC

3ryc


Resolution: 2.22→39.19 Å / σ(F): 1.38 / Phase error: 21.33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.194 5421 5.17 %
Rwork0.159 --
obs0.161 104776 96.1 %
all-104780 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.8 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0205 Å20 Å23.1566 Å2
2--8.373 Å2-0 Å2
3----6.3526 Å2
Refinement stepCycle: LAST / Resolution: 2.22→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15529 0 132 345 16006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116039
X-RAY DIFFRACTIONf_angle_d0.80421824
X-RAY DIFFRACTIONf_dihedral_angle_d14.5275786
X-RAY DIFFRACTIONf_chiral_restr0.0582438
X-RAY DIFFRACTIONf_plane_restr0.0042842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3291X-RAY DIFFRACTIONPOSITIONAL0.109
12D3291X-RAY DIFFRACTIONPOSITIONAL0.109
21A3224X-RAY DIFFRACTIONPOSITIONAL0.139
22C3224X-RAY DIFFRACTIONPOSITIONAL0.139
31E1131X-RAY DIFFRACTIONPOSITIONAL0.01
32F1131X-RAY DIFFRACTIONPOSITIONAL0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2196-2.25790.28332580.2364851X-RAY DIFFRACTION90
2.2579-2.29890.24842600.23494927X-RAY DIFFRACTION91
2.2989-2.34310.26122530.22714928X-RAY DIFFRACTION91
2.3431-2.39090.26722700.22175012X-RAY DIFFRACTION91
2.3909-2.44290.23862580.21124920X-RAY DIFFRACTION91
2.4429-2.49970.25772600.21754981X-RAY DIFFRACTION91
2.4997-2.56220.24112610.20984977X-RAY DIFFRACTION92
2.5622-2.63150.25252550.19934954X-RAY DIFFRACTION92
2.6315-2.70890.26912680.20114991X-RAY DIFFRACTION92
2.7089-2.79630.26972570.19725002X-RAY DIFFRACTION92
2.7963-2.89630.24762580.19084984X-RAY DIFFRACTION92
2.8963-3.01220.24452600.18015001X-RAY DIFFRACTION92
3.0122-3.14920.21192650.17145003X-RAY DIFFRACTION92
3.1492-3.31520.1992650.16344990X-RAY DIFFRACTION92
3.3152-3.52270.21092580.15564998X-RAY DIFFRACTION92
3.5227-3.79450.15522660.13465007X-RAY DIFFRACTION91
3.7945-4.1760.14262590.11984989X-RAY DIFFRACTION92
4.176-4.77940.1582550.10685058X-RAY DIFFRACTION91
4.7794-6.0180.15942580.13484922X-RAY DIFFRACTION90
6.018-39.19780.13952750.13675038X-RAY DIFFRACTION90
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)
10.8742-0.1363-0.09650.75960.41661.7158-0.0102-0.0662-0.0960.01070.0056-0.03090.12280.1458-0.00720.0948-0.006-0.04290.12550.00070.18148.824610.3846-47.882
21.54580.2410.1621.26550.0191.50060.06430.30490.1757-0.071-0.11450.1246-0.0857-0.010.05750.186-0.0255-0.0190.24690.01390.213235.652820.8709-58.4517
30.6544-0.0682-0.50410.40540.19761.8810.04040.11050.0419-0.1175-0.07560.1451-0.1578-0.1980.03910.11-0.0015-0.08110.1421-0.01240.209933.093422.4836-53.848
41.9291-1.50531.48012.7325-2.31523.9464-0.1272-0.12660.34240.0715-0.01-0.1282-0.49290.30260.15590.2511-0.0976-0.07810.1144-0.08960.27843.969731.5903-35.0257
51.10170.3153-0.04491.60360.73561.2641-0.0141-0.02-0.55840.00940.0343-0.03930.55110.2169-0.01340.40210.1631-0.03340.27060.03590.484945.6672-11.4525-13.6454
61.0837-0.05280.22771.49360.03231.18070.0312-0.1568-0.18310.098-0.0758-0.19520.23150.2980.01920.21680.0237-0.07450.32510.06730.183444.04961.2184-5.3771
71.0324-0.16330.17820.9343-0.46621.85060.02070.0473-0.3776-0.15390.12320.13920.1164-0.1522-0.08860.1797-0.0352-0.06640.2362-0.01720.267228.24836.4951-18.3007
81.2796-0.05650.02040.35840.20811.60550.1537-0.0502-0.09870.2058-0.1885-0.1092-0.36490.48820.04840.2904-0.1118-0.06950.40770.00960.251840.572717.81934.3699
90.80180.03770.0180.50140.26342.1175-0.0385-0.08490.1077-0.00330.03580.0524-0.1750.44280.01050.1203-0.0225-0.06220.2207-0.00140.1769-4.056716.388-13.1738
101.4088-0.3045-0.09341.01780.08651.15460.03650.13770.05980.0061-0.07690.11060.0516-0.00470.06740.1791-0.0113-0.04520.24970.02870.243-17.50477.0389-1.7637
110.34270.38310.00690.43780.17312.43310.0419-0.1335-0.10490.1043-0.15240.1160.1562-0.23340.09180.16060.0105-0.0430.17560.03480.1791-19.57115.1217-6.9337
122.72551.9199-2.55643.1051-2.53265.32910.1114-0.1257-0.2652-0.0846-0.1474-0.07530.36060.26840.08870.27950.0453-0.07150.2382-0.03960.242-8.8414-4.4704-25.4011
130.7519-0.3018-0.14941.45660.14421.44850.0274-0.14280.14490.1941-0.0066-0.198-0.55320.19890.01990.2827-0.1806-0.12640.13960.03520.3256-6.841338.1-42.2185
140.8298-0.1924-0.42990.64690.43211.60930.09630.070.1841-0.0482-0.0936-0.1212-0.28710.32080.00870.2365-0.0652-0.03510.14070.03070.2673-6.866427.9865-54.9299
151.0767-0.0070.03890.5258-0.59071.790.0333-0.13810.06660.0620.01920.1441-0.2032-0.2704-0.03020.19040.0144-0.02910.2149-0.01110.2279-23.718220.9357-42.0517
161.09610.0007-0.09420.66360.02112.14720.04570.1038-0.0515-0.1048-0.1381-0.0810.31410.17380.0850.30020.0591-0.04420.1478-0.00740.2059-11.71469.086-64.636
171.9249-0.0858-1.09651.92420.34024.22610.05080.25730.2033-0.6294-0.0953-0.7645-0.27390.21010.10370.4856-0.11270.05380.27930.04680.2571-6.11920.0222-96.7256
181.36290.1517-0.35970.90380.47662.2505-0.1324-0.02140.0392-0.09770.05880.0808-0.0839-0.08320.0530.27190.0692-0.04520.28040.00870.1907-21.724316.1063-86.2781
191.3844-0.2460.0462.51820.78942.0765-0.2627-0.027-0.13010.120.05110.61850.0348-0.68120.18610.315-0.02660.09310.50040.03740.3414-33.288413.1592-69.9207
202.9372-0.53070.83253.44310.67895.59420.12490.1788-0.2292-0.09810.0518-0.39330.19330.3862-0.12210.3505-0.0305-0.09820.63070.04460.363646.36297.504333.7971
211.24230.0901-0.20291.52470.41332.2978-0.13380.0037-0.03020.10360.00320.06220.0649-0.13710.09750.2922-0.0688-0.09850.31430.0420.142130.7610.746326.8295
220.6660.6780.53223.50771.15662.4068-0.1390.586-0.3497-0.21590.0681-0.0955-0.4437-0.33830.04470.3545-0.0021-0.19910.8666-0.05870.527919.448813.21228.3584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:244)
2X-RAY DIFFRACTION2(chain A and resid 245:301)
3X-RAY DIFFRACTION3(chain A and resid 302:407)
4X-RAY DIFFRACTION4(chain A and resid 408:437)
5X-RAY DIFFRACTION5(chain B and resid 1:88)
6X-RAY DIFFRACTION6(chain B and resid 89:249)
7X-RAY DIFFRACTION7(chain B and resid 250:393)
8X-RAY DIFFRACTION8(chain B and resid 394:441)
9X-RAY DIFFRACTION9(chain C and resid 2:244)
10X-RAY DIFFRACTION10(chain C and resid 245:301)
11X-RAY DIFFRACTION11(chain C and resid 302:407)
12X-RAY DIFFRACTION12(chain C and resid 408:437)
13X-RAY DIFFRACTION13(chain D and resid 1:59)
14X-RAY DIFFRACTION14(chain D and resid 60:248)
15X-RAY DIFFRACTION15(chain D and resid 249:393)
16X-RAY DIFFRACTION16(chain D and resid 394:441)
17X-RAY DIFFRACTION17(chain E and resid 13:37)
18X-RAY DIFFRACTION18(chain E and resid 38:137)
19X-RAY DIFFRACTION19(chain E and resid 138:168)
20X-RAY DIFFRACTION20(chain F and resid 13:28)
21X-RAY DIFFRACTION21(chain F and resid 29:142)
22X-RAY DIFFRACTION22(chain F and resid 143:167)

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  • 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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