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Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in presence of adp.alfx (NECK-LINKER IN ITS DISCONNECTED CONFORMATION, based on cryo-electron microscopy experiment

by single particle reconstruction, at 9.2 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-2533, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4ck7
TitlePseudo-atomic model of microtubule-bound human kinesin-5 motor domain in presence of adp.alfx (NECK-LINKER IN ITS DISCONNECTED CONFORMATION, based on cryo-electron microscopy experiment
DescriptorTUBULIN ALPHA-1D CHAIN
TUBULIN BETA-2B CHAIN
KINESIN-LIKE PROTEIN KIF11
KeywordsMOTOR PROTEIN, KINESINS, MICROTUBULES, MITOSIS, MECHANOCHEMISTRY
AuthorsGoulet, A., Major, J., Jun, Y., Gross, S., Rosenfeld, S., Moores, C.
DateDeposition: 2013-12-30, Release: 2014-02-05
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Sequence detailsCYS-LITE MUTANT CONTAINING THE SUBSTITUTION T126C
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-2533, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-2533

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Fit: target map of fitting

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 111, Issue 5, Page 1837-1842, Year 2014
TitleComprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family.
AuthorsAdeline Goulet, Jennifer Major, Yonggun Jun, Steven P Gross, Steven S Rosenfeld, Carolyn A Moores
Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, United Kingdon.
KeywordsAdenosine Diphosphate (metabolism), Adenosine Triphosphate (metabolism), Humans, Hydrolysis, Kinesin (chemistry, 3.6.4.4), Kinetics, Microtubules (metabolism), Mitosis, Models, Molecular, Protein Binding, Protein Structure, Tertiary, Sequence Deletion, Structure-Activity Relationship
LinksPubMed: 24449904, DOI: 10.1073/pnas.1319848111, PMC: PMC3918802
Components
ID 1 : ALPHA TUBULIN
Image
DescriptionTUBULIN ALPHA-1D CHAIN
Typepolypeptide(L)
Formula weight50236.352 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Common name: CATTLE
Alt source flag: sample
NCBI taxonomy: ID:9913
Organ: BRAIN
Organism scientific: BOS TAURUS

LinksUniProt: Q2HJ86, Sequence view
ID 2 : BETA TUBULIN
Image
DescriptionTUBULIN BETA-2B CHAIN
Typepolypeptide(L)
Formula weight49907.770 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
Common name: CATTLE
Alt source flag: sample
NCBI taxonomy: ID:9913
Organ: BRAIN
Organism scientific: BOS TAURUS
LinksUniProt: Q6B856, Sequence view
ID 3 : KINESIN-LIKE PROTEIN 1, KINESIN-LIKE SPINDLE PROTEIN HKSP, KINESIN-RELATED MOTOR PROTEIN EG5, THYROID RECEPTOR-INTERACTING PROTEIN 5, TR-INTERACTING PROTEIN 5, TRIP-5, KINESIN-5
Image
DescriptionKINESIN-LIKE PROTEIN KIF11
Typepolypeptide(L)
FragmentMOTOR DOMAIN, RESIDUES 1-367
MutationYES
Formula weight41673.105 Da
Number of molecules1
ID3
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: HUMAN, ID:9606, HOMO SAPIENS
Alt source flag: sample
Host: ID:511693, ESCHERICHIA COLI

, BL21, PLASMID
Plasmid name: PET21A
LinksUniProt: P52732, Sequence view
ID 4 : MAGNESIUM ION
Image
DescriptionMAGNESIUM ION
Typenon-polymer
Formula weight24.305 Da
Number of molecules2
ID4
SourceMethod: Obtained synthetically
ID 5 : GUANOSINE-5'-TRIPHOSPHATE
Image
DescriptionGUANOSINE-5'-TRIPHOSPHATE
Typenon-polymer
Formula weight523.180 Da
Number of molecules1
ID5
SourceMethod: Obtained synthetically
ID 6 : GUANOSINE-5'-DIPHOSPHATE
Image
DescriptionGUANOSINE-5'-DIPHOSPHATE
Typenon-polymer
Formula weight443.201 Da
Number of molecules1
ID6
SourceMethod: Obtained synthetically
ID 7 : TAXOL
Image
DescriptionTAXOL
Typenon-polymer
Formula weight853.906 Da
Number of molecules1
ID7
SourceMethod: Obtained synthetically
ID 8 : ALUMINUM FLUORIDE
Image
DescriptionALUMINUM FLUORIDE
Typenon-polymer
Formula weight83.977 Da
Number of molecules1
ID8
SourceMethod: Obtained synthetically
ID 9 : ADENOSINE-5'-DIPHOSPHATE
Image
DescriptionADENOSINE-5'-DIPHOSPHATE
Typenon-polymer
Formula weight427.201 Da
Number of molecules1
ID9
SourceMethod: Obtained synthetically
Sample
Entity assembly
NameMICROTUBULE-BOUND HUMAN KINESIN-5 MOTOR DOMAIN
TypeCOMPLEX
Buffer
Specimen id1
Details80 MM PIPES 5 MM MGCL2 1 MM EGTA 1 MM TCEP
Name80 MM PIPES 5 MM MGCL2 1 MM EGTA 1 MM TCEP
PH6.8
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
DetailsHOLEY CARBON
Vitrification
Specimen id1
Cryogen nameETHANE
DetailsLIQUID ETHANE
InstrumentFEI VITROBOT MARK I
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F20
Date2011-03-10
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 50000 X
CsNominal: 2.0 mm
Nominal defocusMax: 2500 nm, Min: 700 nm
Specimen holder
Temperature90 Kelvin
Image scans
Image recording id1
Number digital images125
Processing
Single particle entity
Image processing id1
Point symmetryC1
3D reconstruction
Image processing id1
DetailsTHE N-TERMINAL SEQUENCE WAS MODELLED USING MODELLER. THE DISCONNECTED CONFORMATION OF THE NECK-LINKER WAS CALCULATED USING A CONJUGATE-GRADIENT ENERGY MINIMIZATION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2533. (DEPOSITION ID: 12198).
Number of particles10692
Resolution9.2 A
Symmetry typePOINT
3D fitting
DetailsMETHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY
Refinement ProtocolFLEXIBLE FIT
Refinement SpaceREAL
Target criteriaCross-correlation coefficient
3D fitting list
3D Fitting ID1
PDB entry ID3HQD
3D fitting list
3D Fitting ID1
PDB entry ID1JFF
Refine
Refine idELECTRON MICROSCOPY
Ls d res high9.20 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high9.20
Total atoms1354
Ligand atoms155
Protein atoms1199
Download
PDB format
Allpdb4ck7.ent.gz
pdb4ck7.ent (uncompressed file)
Header onlypdb4ck7.ent.gz
mmCIF format
mmCIF4ck7.cif.gz
XML format
All4ck7.xml.gz
No-atom4ck7-noatom.xml.gz
Ext-atom4ck7-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.4 MB