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- PDB-1tub: TUBULIN ALPHA-BETA DIMER, ELECTRON DIFFRACTION -

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Basic information

Entry
Database: PDB / ID: 1tub
TitleTUBULIN ALPHA-BETA DIMER, ELECTRON DIFFRACTION
Components(TUBULIN) x 2
KeywordsMICROTUBULES / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE
Function / homology
Function and homology information


structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase 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 ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase 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 / 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 / TAXOTERE / Tubulin alpha-1A chain / Tubulin beta chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.7 Å
AuthorsNogales, E. / Downing, K.H.
Citation
Journal: Nature / Year: 1998
Title: Structure of the alpha beta tubulin dimer by electron crystallography.
Authors: E Nogales / S G Wolf / K H Downing /
Abstract: The alphabeta tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each ...The alphabeta tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each tubulin monomer binds a guanine nucleotide, which is nonexchangeable when it is bound in the alpha subunit, or N site, and exchangeable when bound in the beta subunit, or E site. The alpha- and beta-tubulins share 40% amino-acid sequence identity, both exist in several isotype forms, and both undergo a variety of posttranslational modifications. Limited sequence homology has been found with the proteins FtsZ and Misato, which are involved in cell division in bacteria and Drosophila, respectively. Here we present an atomic model of the alphabeta tubulin dimer fitted to a 3.7-A density map obtained by electron crystallography of zinc-induced tubulin sheets. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three functional domains: the amino-terminal domain containing the nucleotide-binding region, an intermediate domain containing the Taxol-binding site, and the carboxy-terminal domain, which probably constitutes the binding surface for motor proteins.
#1: Journal: Nature / Year: 1998
Title: Erratum. Structure of the Alpha Beta Tubulin Dimer by Electron Crystallography
Authors: Nogales, E. / Wolf, S.G. / Downing, K.H.
#2: Journal: Nat.Struct.Biol. / Year: 1998
Title: Tubulin and Ftsz Form a Distinct Family of Gtpases
Authors: Nogales, E. / Downing, K.H. / Amos, L.A. / Lowe, J.
History
DepositionSep 23, 1997Processing site: BNL
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Data processing / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation / em_3d_reconstruction / em_image_scans / em_single_particle_entity / pdbx_database_status / 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 / _diffrn_radiation.pdbx_scattering_type / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: TUBULIN
B: TUBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5845
Polymers96,8102
Non-polymers1,7743
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-30 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.000, 92.000, 90.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TUBULIN


Mass: 48869.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: BRAIN / References: UniProt: P02550
#2: Protein TUBULIN


Mass: 47940.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: BRAIN / References: UniProt: P02554
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-TXL / TAXOTERE


Mass: 807.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H53NO14 / Comment: medication, chemotherapy*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: alpha-beta tubulin sheets / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: tannin-glucose
CrystalDescription: THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB- ...Description: THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE.
Crystal growDetails: TWO-DIMENSIONAL SHEETS ARE FORMED UNDER NORMAL POLYMERIZING CONDITIONS WITH THE ADDITION OF 1 MM ZNCL2
Crystal grow
*PLUS
Method: unknown

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Data collection

EM imaging
IDAccelerating voltage (kV)Electron sourceIllumination modeModelModeSpecimen-ID
1400FIELD EMISSION GUNFLOOD BEAMJEOL 4000DIFFRACTION1
2400FIELD EMISSION GUNSPOT SCANJEOL 4000BRIGHT FIELD1
Image recordingFilm or detector model: GENERIC FILM
DetectorDate: Sep 1, 1996
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Rmerge(I) obs: 0.25

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Processing

RefinementHighest resolution: 3.7 Å
Details: THESE INITIAL COORDINATES ARE FOR THE MODEL BUILT IN THE ORIGINAL DENSITY MAP, WITH NO REFINEMENT.
Refinement stepCycle: LAST / Highest resolution: 3.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6789 0 118 0 6907

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