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- PDB-2wbe: Kinesin-5-Tubulin Complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 2wbe
TitleKinesin-5-Tubulin Complex with AMPPNP
Components
  • BIPOLAR KINESIN KRP-130
  • TUBULIN ALPHA-1D CHAIN
  • TUBULIN BETA-2B CHAIN
KeywordsSTRUCTURAL PROTEIN / EG5 / KLP61F / KINESIN / TUBULIN / MITOSIS / KINESIN-5 / GTP-BINDING / MOTOR PROTEIN / CELL DIVISION / CELL CYCLE / MICROTUBULE / ATP-BINDING / HOMOLOGY MODEL / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING
Function / homologyTubulin/FtsZ, GTPase domain / Kinesin motor domain superfamily / Tubulin / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain ...Tubulin/FtsZ, GTPase domain / Kinesin motor domain superfamily / Tubulin / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Kinesin motor domain, conserved site / Tubulin, C-terminal / Kinesin-associated microtubule-binding domain / P-loop containing nucleoside triphosphate hydrolase / Kinesin-like protein / Tubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Intraflagellar transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Recycling pathway of L1 / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / MHC class II antigen presentation / Kinesin motor domain profile. / Tubulin/FtsZ family, GTPase domain / Kinesin motor domain signature. / Tubulin-beta mRNA autoregulation signal. / Tubulin subunits alpha, beta, and gamma signature. / Kinesin-associated microtubule-binding / Tubulin C-terminal domain / Kinesin motor domain / Cilium Assembly / Hedgehog 'off' state / COPI-mediated anterograde transport / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / The role of GTSE1 in G2/M progression after G2 checkpoint / Carboxyterminal post-translational modifications of tubulin / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Hedgehog 'on' state / Kinesins / Kinesins / aster / plus-end directed microtubule sliding / adult chitin-containing cuticle pigmentation / fusome organization / fusome / mitotic spindle microtubule / centrosome separation / positive regulation of Golgi to plasma membrane protein transport / ATP-dependent microtubule motor activity, plus-end-directed / microtubule bundle formation / positive regulation of axon guidance / microtubule associated complex / Golgi organization / mitotic centrosome separation / mitotic spindle pole / kinesin complex / protein secretion / motor activity / mitotic spindle assembly / microtubule-based process / microtubule motor activity / mitotic spindle / mitotic spindle organization / microtubule-based movement / structural constituent of cytoskeleton / neuron migration / chromosome segregation / microtubule cytoskeleton / spindle / mitotic cell cycle / protein homotetramerization / microtubule / microtubule binding / GTPase activity / cell division / GTP binding / protein heterodimerization activity / endoplasmic reticulum / Golgi apparatus / ATP binding / nucleus / cytoplasm / Tubulin alpha-1A chain / Tubulin beta chain / Kinesin-like protein Klp61F / Tubulin alpha-1D chain / Tubulin beta-2B chain
Function and homology information
Specimen sourceDROSOPHILA MELANOGASTER (fruit fly)
BOS TAURUS (cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 9.4 Å resolution
AuthorsBodey, A.J. / Kikkawa, M. / Moores, C.A.
CitationJournal: J. Mol. Biol. / Year: 2009
Title: 9-Angström structure of a microtubule-bound mitotic motor.
Authors: Andrew J Bodey / Masahide Kikkawa / Carolyn A Moores
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2009 / Release: Mar 24, 2009
RevisionDateData content typeGroupProviderType
1.0Mar 24, 2009Structure modelrepositoryInitial release
1.1Jul 24, 2013Structure modelDatabase references / Derived calculations / Other / Refinement description / Source and taxonomy / Version format compliance
1.2Jul 27, 2016Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
1.3Apr 19, 2017Structure modelOther
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Assembly

Deposited unit
A: TUBULIN ALPHA-1D CHAIN
B: TUBULIN BETA-2B CHAIN
C: BIPOLAR KINESIN KRP-130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3029
Polyers141,9273
Non-polymers2,3756
Water0
1
A: TUBULIN ALPHA-1D CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6553
Polyers50,1071
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TUBULIN BETA-2B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2053
Polyers49,9081
Non-polymers1,2972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BIPOLAR KINESIN KRP-130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4423
Polyers41,9121
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

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Protein/peptide , 3 types, 3 molecules ABC

#1: Protein/peptide TUBULIN ALPHA-1D CHAIN / ALPHA-BETA-TUBULIN / TUBA1D


Mass: 50107.238 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: P02550, UniProt: Q2HJ86*PLUS
#2: Protein/peptide TUBULIN BETA-2B CHAIN / ALPHA-BETA-TUBULIN / TUBB2B


Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: P02554, UniProt: Q6B856*PLUS
#3: Protein/peptide BIPOLAR KINESIN KRP-130 / KLP61F / KINESIN-LIKE PROTEIN KLP61F / KLP2


Mass: 41911.566 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN WITH NECK LINKER, RESIDUES 1-368 / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid name: PET-15B-TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46863

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14 / Paclitaxel
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM

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Details

Nonpolymer detailsPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP): NON-HYDROLYSABLE ATP ANALOGUE

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: MICROTUBULE-KLP61F COMPLEX WITH AMPPNP / Type: COMPLEX
Buffer solutionName: 80MM PIPES, 150MM NACL, 7MM MGCL2, 1MM EGTA, 1MM BETA-MERCAPTOETHANOL
Details: 80MM PIPES, 150MM NACL, 7MM MGCL2, 1MM EGTA, 1MM BETA-MERCAPTOETHANOL
pH: 6.8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Calibrated magnification: 50000 / Nominal defocus max: 3940 nm / Nominal defocus min: 1080 nm / Cs: 2 mm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 24

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Processing

EM softwareName: RUBY-HELIX / Category: 3D reconstruction
CTF correctionDetails: PHASE FLIPPING, WIENER
3D reconstructionMethod: HELICAL PROCESSING / Resolution: 9.4 Å / Nominal pixel size: 1.4 / Actual pixel size: 1.4
Details: THE KLP61F HOMOLOGY MODEL WAS GENERATED WITH MODELLER 9V1 AND THE FOLLOWING TEMPLATES - 1MKJ.PDB, 1T5C.PDB AND 2KIN.PDB
Symmetry type: HELICAL
Atomic model buildingDetails: REFINEMENT PROTOCOL--HOMOLOGY (KLP61F), ELECTRON CRYSTALLOGRAPHY (TUBULIN)
Ref protocol: OTHER
Atomic model building
IDPDB-ID 3D fitting ID
11MKJ1
21T5C1
32KIN1
Least-squares processHighest resolution: 9.4 Å
Refine hist #LASTHighest resolution: 9.4 Å
Number of atoms included #LASTProtein: 9230 / Nucleic acid: 0 / Ligand: 155 / Solvent: 0 / Total: 9385

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