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- PDB-4f61: Tubulin:Stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 4f61
TitleTubulin:Stathmin-like domain complex
Components
  • Stathmin-like domain R4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / RB3 / STATHMIN TUBULIN
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 / synapse organization / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / cerebral cortex development / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / 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 / cytoplasm / cytosol
Similarity search - Function
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-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
GUANOSINE-5'-DIPHOSPHATE / 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: 4.17 Å
AuthorsGigant, B. / Mignot, I. / Knossow, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Design and characterization of modular scaffolds for tubulin assembly.
Authors: Mignot, I. / Pecqueur, L. / Dorleans, A. / Karuppasamy, M. / Ravelli, R.B. / Dreier, B. / Pluckthun, A. / Knossow, M. / Gigant, B.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 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.ptnr1_label_seq_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.ptnr3_label_seq_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Tubulin alpha chain
F: Tubulin beta chain
G: Tubulin alpha chain
H: Tubulin beta chain
I: Stathmin-like domain R4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)433,49821
Polymers429,5369
Non-polymers3,96312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30490 Å2
ΔGint-131 kcal/mol
Surface area130410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)639.740, 66.100, 128.130
Angle α, β, γ (deg.)90.00, 92.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 9 molecules ACEGBDFHI

#1: Protein
Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWZ0
#2: Protein
Tubulin beta chain


Mass: 49983.824 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWY9
#3: Protein Stathmin-like domain R4


Mass: 28782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artificial gene (others) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 3 types, 12 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: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Details

Sequence detailsAUTHOR STATES THAT THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE ...AUTHOR STATES THAT THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR ALPHA-TUBULIN (CHAINS A,C,E,G) THEY USED THE ALPHA 1B ISOTYPE SEQUENCE (NCBI NP_001108328.1). FOR BETA-TUBULIN (CHAINS B,D,F,H), THEY USED THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_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: 3.16 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG, NACL, PIPES BUFFER, PH 6.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.17→50 Å / Num. all: 40900 / Num. obs: 40336 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 125.69 Å2 / Rsym value: 0.112 / Net I/σ(I): 8.2
Reflection shellResolution: 4.17→4.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.65 / Rsym value: 0.876 / % possible all: 90.8

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RYC

3ryc


Resolution: 4.17→49.04 Å / Cor.coef. Fo:Fc: 0.8202 / Cor.coef. Fo:Fc free: 0.8021 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2024 5.02 %RANDOM
Rwork0.2411 ---
obs0.2421 40332 98.58 %-
Displacement parametersBiso mean: 182.8 Å2
Baniso -1Baniso -2Baniso -3
1-111.919 Å20 Å229.4641 Å2
2---12.7256 Å20 Å2
3----99.1934 Å2
Refine analyzeLuzzati coordinate error obs: 1.417 Å
Refinement stepCycle: LAST / Resolution: 4.17→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28885 0 244 0 29129
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0129764HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.240385HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10319SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes804HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4421HARMONIC5
X-RAY DIFFRACTIONt_it29764HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion19.73
X-RAY DIFFRACTIONt_chiral_improper_torsion3883SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact33430SEMIHARMONIC4
LS refinement shellResolution: 4.17→4.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3136 140 5.28 %
Rwork0.2867 2512 -
all0.2881 2652 -
obs--98.58 %
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)
15.73311.04111.29911.5650.65741.4877-0.11721.0824-0.03670.05140.1528-0.25650.11-0.0375-0.03570.25080.10680.0146-0.109-0.3004-0.5878-135.0902-21.793711.582
26.61470.2799-0.49183.05860.03421.7226-0.04140.61770.60070.0873-0.09110.04140.18190.06010.13250.01750.17570.0186-0.0662-0.298-0.6074-99.35061.954416.3896
33.59191.3982.32050.95351.31080.1592-0.0058-0.88311.068-0.4497-0.60760.33240.0368-0.05070.6134-0.51190.2098-0.21540.608-0.29680.5941-60.299519.95724.4052
43.00171.38240.51070.07251.06360.03230.1219-0.40251.0746-0.3125-0.67670.27740.0022-0.17020.5547-0.43890.1887-0.26880.608-0.18540.5903-20.117829.334730.9367
52.4391-0.90912.180700.18420.1508-0.1548-0.35610.6874-0.3529-0.0756-0.13790.007-0.33770.2305-0.38280.2476-0.15410.6080.31280.598222.600631.448540.7461
61.8712-0.010.36191.18950.46540.39030.1112-0.04380.5105-0.0959-0.1599-0.2161-0.1471-0.64690.0487-0.36880.2315-0.11680.35440.31220.488263.267924.515147.7368
72.4722-1.12591.10211.707-0.36530.0747-0.25230.0390.46710.04870.343-0.2011-0.0524-0.398-0.0907-0.02410.19330.1035-0.13060.15320.1126103.65229.714257.0006
82.9487-0.75150.87955.10950.22423.5046-0.05680.24540.31330.08750.0741-0.6283-0.1208-0.3836-0.0173-0.1522-0.00760.2063-0.608-0.0227-0.3536138.8686-12.140463.2837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|438 A|600 - A|601 I|4 - I|64 }A1 - 438
2X-RAY DIFFRACTION1{ A|1 - A|438 A|600 - A|601 I|4 - I|64 }A600 - 601
3X-RAY DIFFRACTION1{ A|1 - A|438 A|600 - A|601 I|4 - I|64 }I4 - 64
4X-RAY DIFFRACTION2{ I|65 - I|89 B|1 - B|442 B|600 - B|600 }I65 - 89
5X-RAY DIFFRACTION2{ I|65 - I|89 B|1 - B|442 B|600 - B|600 }B1 - 442
6X-RAY DIFFRACTION2{ I|65 - I|89 B|1 - B|442 B|600 - B|600 }B600
7X-RAY DIFFRACTION3{ I|90 - I|115 C|1 - C|439 C|600 - C|601 }I90 - 115
8X-RAY DIFFRACTION3{ I|90 - I|115 C|1 - C|439 C|600 - C|601 }C1 - 439
9X-RAY DIFFRACTION3{ I|90 - I|115 C|1 - C|439 C|600 - C|601 }C600 - 601
10X-RAY DIFFRACTION4{ I|116 - I|140 D|1 - D|442 D|600 - D|600 }I116 - 140
11X-RAY DIFFRACTION4{ I|116 - I|140 D|1 - D|442 D|600 - D|600 }D1 - 442
12X-RAY DIFFRACTION4{ I|116 - I|140 D|1 - D|442 D|600 - D|600 }D600
13X-RAY DIFFRACTION5{ I|141 - I|164 E|1 - E|439 E|600 - E|601 }I141 - 164
14X-RAY DIFFRACTION5{ I|141 - I|164 E|1 - E|439 E|600 - E|601 }E1 - 439
15X-RAY DIFFRACTION5{ I|141 - I|164 E|1 - E|439 E|600 - E|601 }E600 - 601
16X-RAY DIFFRACTION6{ I|165 - I|191 F|1 - F|442 F|600 - F|600 }I165 - 191
17X-RAY DIFFRACTION6{ I|165 - I|191 F|1 - F|442 F|600 - F|600 }F1 - 442
18X-RAY DIFFRACTION6{ I|165 - I|191 F|1 - F|442 F|600 - F|600 }F600
19X-RAY DIFFRACTION7{ I|192 - I|217 G|1 - G|439 G|600 - G|601 }I192 - 217
20X-RAY DIFFRACTION7{ I|192 - I|217 G|1 - G|439 G|600 - G|601 }G1 - 439
21X-RAY DIFFRACTION7{ I|192 - I|217 G|1 - G|439 G|600 - G|601 }G600 - 601
22X-RAY DIFFRACTION8{ I|218 - I|243 H|1 - H|441 H|600 - H|600 }I218 - 243
23X-RAY DIFFRACTION8{ I|218 - I|243 H|1 - H|441 H|600 - H|600 }H1 - 441
24X-RAY DIFFRACTION8{ I|218 - I|243 H|1 - H|441 H|600 - H|600 }H600

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