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- PDB-3n2k: TUBULIN-NSC 613862: RB3 Stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 3n2k
TitleTUBULIN-NSC 613862: RB3 Stathmin-like domain complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / COLCHICINE DOMAIN / COVALENT BINDING / MICROTUBULE / 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 / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / condensed chromosome / response to mechanical stimulus / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / intracellular protein transport / neuron migration / synapse organization / visual learning / neuromuscular junction / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-K2N / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
OVIS ARIES (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBarbier, P. / Dorleans, A. / Devred, F. / Sanz, L. / Allegro, D. / Alfonso, C. / Knossow, M. / Peyrot, V. / Andreu, J.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Stathmin and interfacial microtubule inhibitors recognize a naturally curved conformation of tubulin dimers.
Authors: Barbier, P. / Dorleans, A. / Devred, F. / Sanz, L. / Allegro, D. / Alfonso, C. / Knossow, M. / Peyrot, V. / Andreu, J.M.
History
DepositionMay 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,68614
Polymers217,0295
Non-polymers2,6569
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-115 kcal/mol
Surface area64910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)326.321, 326.321, 54.057
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 243
2111C2 - 243
1211A257 - 439
2211C257 - 439
1121B2 - 273
2121D2 - 273

NCS ensembles :
ID
1
2

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50188.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / Organ: BRAIN / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / Organ: BRAIN / References: UniProt: D0VWY9
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16712.967 Da / Num. of mol.: 1 / Fragment: UNP residues 49-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Gene: STMN4 / Plasmid: PET-8C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63043

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Non-polymers , 4 types, 9 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: 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
#7: Chemical ChemComp-K2N / ethyl [(2S)-5-amino-2-methyl-3-phenyl-1,2-dihydropyrido[3,4-b]pyrazin-7-yl]carbamate


Mass: 325.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N5O2

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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: 3.83 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: PEG, PIPES BUFFER, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.935
DetectorType: ADSC / Detector: CCD / Date: Nov 10, 2006
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 28503 / % possible obs: 99.6 % / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 20
Reflection shellResolution: 4→4.1 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.621 / % possible all: 99.7

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SA0

1sa0


Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / SU B: 47.857 / SU ML: 0.609 / Cross valid method: THROUGHOUT / ESU R Free: 0.74 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25012 1435 5.1 %RANDOM
Rwork0.22318 ---
obs0.22461 26934 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 232.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14054 0 171 0 14225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02114539
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.95419770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.81451817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.22178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211189
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.27428
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3240.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1821.59080
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.354214553
X-RAY DIFFRACTIONr_scbond_it0.60635459
X-RAY DIFFRACTIONr_scangle_it0.9934.55217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3090tight positional0.060.05
2B2043tight positional0.060.05
1A3090tight thermal0.070.5
2B2043tight thermal0.080.5
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 106
Rwork0.346 1917
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)
110.38162.24480.10623.0856-0.41153.42360.1992-0.8730.97790.0296-0.2499-0.2298-0.45050.28480.05071.2885-0.13480.09761.38860.04011.5965134.9113105.307717.1171
211.20922.527-0.5655.0535-0.99944.1958-0.27190.251-0.5481-0.6732-0.0742-0.17040.4162-0.23540.34611.4118-0.2959-0.12471.73620.13281.0605101.135681.61335.1374
39.89882.5135-0.12064.9297-0.33434.6095-0.30510.393-0.5794-0.85640.2701-0.3328-0.04630.80440.0351.5009-0.2627-0.47471.96260.33661.415663.562161.9056-2.6832
49.59332.7889-0.35996.413-0.51446.4487-0.68650.66880.0989-0.6704-0.5761.17370.4115-0.47181.26241.1164-0.0932-1.32662.22730.0561.577724.496647.8711-6.1837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 601
2X-RAY DIFFRACTION1E4 - 64
3X-RAY DIFFRACTION2B2 - 700
4X-RAY DIFFRACTION2E65 - 89
5X-RAY DIFFRACTION3C2 - 601
6X-RAY DIFFRACTION3E90 - 115
7X-RAY DIFFRACTION4D2 - 700
8X-RAY DIFFRACTION4E116 - 141

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