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- PDB-1ia0: KIF1A HEAD-MICROTUBULE COMPLEX STRUCTURE IN ATP-FORM -

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Basic information

Entry
Database: PDB / ID: 1ia0
TitleKIF1A HEAD-MICROTUBULE COMPLEX STRUCTURE IN ATP-FORM
Components
  • KINESIN-LIKE PROTEIN KIF1A
  • TUBULIN ALPHA CHAIN
  • TUBULIN BETA CHAIN
KeywordsTRANSPORT PROTEIN / tubulin / microtubule / KIF1A / FITTING OF X-RAY STRUCTURES INTO CRYO-EM RECONSTRUCTIONS
Function / homology
Function and homology information


anterograde synaptic vesicle transport / neuronal dense core vesicle membrane / plus-end-directed kinesin ATPase / dense core granule cytoskeletal transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development / regulation of dendritic spine morphogenesis / MHC class II antigen presentation / plus-end-directed microtubule motor activity ...anterograde synaptic vesicle transport / neuronal dense core vesicle membrane / plus-end-directed kinesin ATPase / dense core granule cytoskeletal transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development / regulation of dendritic spine morphogenesis / MHC class II antigen presentation / plus-end-directed microtubule motor activity / motile cilium / neuronal dense core vesicle / axon cytoplasm / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / neuron projection / neuronal cell body / GTPase activity / synapse / GTP binding / perinuclear region of cytoplasm / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / PH domain / Kinesin motor domain superfamily / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOTERE / Tubulin alpha-1A chain / Tubulin beta chain / Kinesin-like protein KIF1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 15 Å
AuthorsKikkawa, M. / Sablin, E.P. / Okada, Y. / Yajima, H. / Fletterick, R.J. / Hirokawa, N.
Citation
Journal: Nature / Year: 2001
Title: Switch-based mechanism of kinesin motors.
Authors: M Kikkawa / E P Sablin / Y Okada / H Yajima / R J Fletterick / N Hirokawa /
Abstract: Kinesin motors are specialized enzymes that use hydrolysis of ATP to generate force and movement along their cellular tracks, the microtubules. Although numerous biochemical and biophysical studies ...Kinesin motors are specialized enzymes that use hydrolysis of ATP to generate force and movement along their cellular tracks, the microtubules. Although numerous biochemical and biophysical studies have accumulated much data that link microtubule-assisted ATP hydrolysis to kinesin motion, the structural view of kinesin movement remains unclear. This study of the monomeric kinesin motor KIF1A combines X-ray crystallography and cryo-electron microscopy, and allows analysis of force-generating conformational changes at atomic resolution. The motor is revealed in its two functionally critical states-complexed with ADP and with a non-hydrolysable analogue of ATP. The conformational change observed between the ADP-bound and the ATP-like structures of the KIF1A catalytic core is modular, extends to all kinesins and is similar to the conformational change used by myosin motors and G proteins. Docking of the ADP-bound and ATP-like crystallographic models of KIF1A into the corresponding cryo-electron microscopy maps suggests a rationale for the plus-end directional bias associated with the kinesin catalytic core.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: 15 Angstrom Resolution Model of the Monomeric Kinesin Motor, KIF1A
Authors: Kikkawa, M. / Okada, Y. / Hirokawa, N.
History
DepositionMar 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 27, 2016Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: refine / Item: _refine.details
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.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.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
Revision 1.6Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE COMPLEX PARTICLE HAS A HELICAL SYMMETRY WITH 15 PROTOFILAMENTS.
Remark 350GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY ...GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. LET P(0,0) = COORDINATES OF ANY ATOM AS LISTED IN ENTRY 1. BIOMT1 1 0.914728 -0.404068 0.000000 0.000000 BIOMT2 1 0.404068 0.914728 0.000000 0.000000 BIOMT3 1 0.000000 0.000000 1.000000 10.592334 APPLY FOLLOWING OPERATOR REPETITIVELY TO GENERATE SHALLOW HELIX. P(N+1,0) = BIOMT 1 * P(N,0) 2. BIOMT1 2 0.999042 0.043771 0.000000 0.000000 BIOMT2 2 -0.043771 0.999042 0.000000 0.000000 BIOMT3 2 0.000000 0.000000 1.000000 79.442509 THEN APPLY FOLLOWING OPERATOR REPETITIVELY TO GENERATE WHOLE KIF1A-MICROTUBULE COMPLEX. P(N,M+1) = BIOMT 2 * P(N,M)

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Structure visualization

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Assembly

Deposited unit
A: TUBULIN ALPHA CHAIN
B: TUBULIN BETA CHAIN
K: KINESIN-LIKE PROTEIN KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6368
Polymers144,3323
Non-polymers2,3045
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules ABK

#1: Protein TUBULIN ALPHA CHAIN


Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
#2: Protein TUBULIN BETA CHAIN


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein KINESIN-LIKE PROTEIN KIF1A


Mass: 44302.855 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Mutation: P202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: KIF1A / Plasmid: PET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33173

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Non-polymers , 5 types, 5 molecules

#4: 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
#5: 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
#6: Chemical ChemComp-TXL / TAXOTERE


Mass: 807.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H53NO14 / Comment: medication, chemotherapy*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: KIF1A HEAD DECORATED MICROTUBULE / Type: COMPLEX
Details: TUBULIN WAS POLYMERIZED IN PEM BUFFER (PIPES 100 MM, PH 6.8, EGTA 1 MM, MGCL2, GTP 1MM, PACLITAXEL 10 MICRO M, 5% DMSO ) FOR 2 HRS AT 37C. A DROP OF THE POLYMERIZED MICROTUBULE WAS PLACED ON ...Details: TUBULIN WAS POLYMERIZED IN PEM BUFFER (PIPES 100 MM, PH 6.8, EGTA 1 MM, MGCL2, GTP 1MM, PACLITAXEL 10 MICRO M, 5% DMSO ) FOR 2 HRS AT 37C. A DROP OF THE POLYMERIZED MICROTUBULE WAS PLACED ON THE HOLEY CARBON FILM ON THE EM-GRID AND LEFT FOR 10 S IN THE HUMID CHAMBER. THE MICROTUBULE SOLUTION WAS THEN ABSORBED BY FILTER PAPER, AND A DROP OF THE C351 SOLUTION (0.2 MG/ML) IN THE ASSAY BUFFER (IMIDAZOLE 50 MM, MG-ACETATE 5 MM, EGTA 1 MM, K-ACETATE 50 MM, DTT 10 MM, PACLITAXEL 10 MICRO M) WAS PUT ON THE GRID. IMMEDIATELY AFTER THE ABSORPTION OF THE DROP, THE GRID WAS PLUNGED INTO LIQUID ETHANE (-185C). THE SAMPLE CONSISTS OF A KIF1A-DECORATED MICROTUBULE. THE EXPERIMENT DESCRIBES A MICROTUBULE-RELATED PROCESS.
Buffer solutionName: buf1 / pH: 7.4
Details: IMIDAZOLE 50 MM, MG-ACETATE 5 MM, EGTA 1 MM, K-ACETATE 50 MM, DTT 10 MM, PACLITAXEL 10 MICRO M
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: PLUNGED INTO ETHANE
Crystal growTemperature: 296 K / Method: polymerization of the microtubule / pH: 6.8
Details: pH 6.8, polymerization of the microtubule, temperature 296K

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Electron microscopy imaging

MicroscopyModel: JEOL 2010F / Date: Jul 1, 1998
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1700 nm / Cs: 3.3 mm
Specimen holderTemperature: 110 K / Tilt angle max: 2 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 130

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Processing

3D reconstructionResolution: 15 Å / Num. of particles: 37000 / Nominal pixel size: 2.5 Å
Details: THREE-DIMENSIONAL RECONSTRUCTION METHOD: FOURIER-BESSEL-TRANSFORM (DEROSIER AND MOORE, 1970 J.MOL.BIOL. 52, 355-369; BEROUKHIM AND UNWIN, 1997 ULTRAMICROSCOPY 70, 57-81). Software used: MRC ...Details: THREE-DIMENSIONAL RECONSTRUCTION METHOD: FOURIER-BESSEL-TRANSFORM (DEROSIER AND MOORE, 1970 J.MOL.BIOL. 52, 355-369; BEROUKHIM AND UNWIN, 1997 ULTRAMICROSCOPY 70, 57-81). Software used: MRC PROGRAMS. EFFECTIVE RESOLUTION OF THE RECONSTRUCTION: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 15 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND CALCULATING THE FOURIER SHELL CORRELATIONS BETWEEN THE TWO INDEPENDENT SET. (HEEL, 1987, ULTRAMICROSCOPY 21, 95-100). 1IA0 is an atomic model of KIF1A head-microtubule complex, which contains KIF1A, alpha-tubulin, and beta-tubulin. Since alpha- and beta-tubulin were indistinguishable at 15A resolution, the assignment of alpha- and beta-tubulin was arbitrary when 1IA0 was deposited. Authors state that they were aware of the limitation and didn't mention about the assignment of alpha- and beta-tubulin in the relevant 2001 Nature paper. Therefore, the main conclusions in the paper are still hold true. However, subsequently the assignment of alpha- and beta-tubulin turned out to be wrong and should be swapped. For the correct assignment and better structures, please use 2HXF. This is based on higher resolution (10 ) structure, which was published in EMBO J. 2006. 25:4187-4194.
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: MAXIMUM CORRELATION / Details: REFINEMENT PROTOCOL--RIGID BODY REFINEMENT
Atomic model buildingPDB-ID: 1TUB

1tub


Accession code: 1TUB / Source name: PDB / Type: experimental model
RefinementHighest resolution: 15 Å
Details: 1IA0 is a atomic model of KIF1A head-microtubule complex, which contains KIF1A, alpha-tubulin, and beta-tubulin. Since alpha- and beta-tubulin were indistinguishable at 15A resolution, the ...Details: 1IA0 is a atomic model of KIF1A head-microtubule complex, which contains KIF1A, alpha-tubulin, and beta-tubulin. Since alpha- and beta-tubulin were indistinguishable at 15A resolution, the assignment of alpha- and beta-tubulin was arbitrary when 1IA0 was deposited. Authors state that they were aware of the limitation and didn't mention about the assignment of alpha- and beta-tubulin in the relevant 2001 Nature paper. Therefore, the main conclusions in the paper are still hold true. However, subsequently the assignment of alpha- and beta-tubulin turned out to be wrong and should be swapped. For the correct assignment and better structures, please use 2HXF. This is based on higher resolution (10 angstrom) structure, which was published in EMBO J. 2006. 25:4187-4194.
Refinement stepCycle: LAST / Highest resolution: 15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9373 0 150 0 9523

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