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- PDB-4hna: Kinesin motor domain in the ADP-MG-ALFX state in complex with tub... -

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Basic information

Entry
Database: PDB / ID: 4hna
TitleKinesin motor domain in the ADP-MG-ALFX state in complex with tubulin and a DARPIN
Components
  • DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2
  • Kinesin-1 heavy chainKinesin
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / alpha-tubulin / beta-tubulin / DARPin / GTPase / kinesin / microtubule / tubulin
Function / homology
Function and homology information


cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / anterograde neuronal dense core vesicle transport / anterograde dendritic transport of neurotransmitter receptor complex / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / axonemal microtubule / organelle transport along microtubule ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / anterograde neuronal dense core vesicle transport / anterograde dendritic transport of neurotransmitter receptor complex / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / vesicle transport along microtubule / neuron projection arborization / lysosome localization / cerebellar cortex morphogenesis / positive regulation of potassium ion transport / dentate gyrus development / natural killer cell mediated cytotoxicity / pyramidal neuron differentiation / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / mitochondrion transport along microtubule / motor behavior / ciliary rootlet / centrosome localization / response to L-glutamate / kinesin complex / synaptic vesicle transport / microtubule motor activity / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / microtubule-based movement / Insulin processing / startle response / microtubule polymerization / centriolar satellite / Signaling by ALK fusions and activated point mutants / response to tumor necrosis factor / Nuclear events stimulated by ALK signaling in cancer / microtubule-based process / phagocytic vesicle / response to mechanical stimulus / homeostasis of number of cells within a tissue / axon cytoplasm / condensed chromosome / cellular response to calcium ion / MHC class II antigen presentation / regulation of membrane potential / dendrite cytoplasm / adult locomotory behavior / axon guidance / positive regulation of synaptic transmission, GABAergic / synapse organization / positive regulation of protein localization to plasma membrane / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / cerebral cortex development / memory / recycling endosome / cellular response to type II interferon / gene expression / microtubule binding / neuron apoptotic process / vesicle / microtubule / hydrolase activity / cadherin binding / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kinesin motor domain / Kinesin / Helix hairpin bin / Kinesin-like protein / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain ...Kinesin motor domain / Kinesin / Helix hairpin bin / Kinesin-like protein / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing 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 / 60s Ribosomal Protein L30; Chain: A; / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain / Kinesin-1 heavy chain
Similarity search - Component
Biological speciesARTIFICIAL GENE (others)
Homo sapiens (human)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsGigant, B. / Knossow, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of a kinesin-tubulin complex and implications for kinesin motility.
Authors: Gigant, B. / Wang, W. / Dreier, B. / Jiang, Q. / Pecqueur, L. / Pluckthun, A. / Wang, C. / Knossow, M.
History
DepositionOct 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_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_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
D: DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2
K: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,17512
Polymers157,5034
Non-polymers1,6728
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.050, 160.540, 174.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABDK

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BRAIN / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 49983.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BRAIN / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWY9
#3: Protein DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2


Mass: 18140.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PDST067 (PQE30 DERIVATIVE) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE
#4: Protein Kinesin-1 heavy chain / Kinesin / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 39174.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33176

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Non-polymers , 6 types, 10 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe sequence of kinesin (chain K) included mutations. The construct is known as cys-lite. for ...The sequence of kinesin (chain K) included mutations. The construct is known as cys-lite. for tubulin the bovine brain tubulin sequence was used for refinement because the sequence of ovine brain tubulin is not available. for alpha-tubulin (chain A) The alpha 1B isotype sequence (NCBI NP_001108328.1) was used. For beta-tubulin (chain B) the beta 2B isotype sequence (NCBI NP_001003900.1) was used.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64 %
Description: DUE TO THE ANISOTROPIC NATURE OF THE DIFFRACTION, THE DATA WERE PROCESSED IN TWO DIFFERENT WAYS: 1) BY APPLYING AN ANISOTROPIC CORRECTION TO THE DATA, AND 2) WITHOUT ANY ANISOTROPY ...Description: DUE TO THE ANISOTROPIC NATURE OF THE DIFFRACTION, THE DATA WERE PROCESSED IN TWO DIFFERENT WAYS: 1) BY APPLYING AN ANISOTROPIC CORRECTION TO THE DATA, AND 2) WITHOUT ANY ANISOTROPY CORRECTION. STRUCTURE FACTORS FOR BOTH PROCESSING HAVE BEEN DEPOSITED WITH THE PDB. THE COORDINATES AND STATISTICS REPORTED HERE ARE THOSE OBTAINED WITH THE DATA CORRECTED FOR ANISOTROPY.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG, PIPES BUFFER, PH 6.8, 0.8 MM ALCL3, 4 MM NAF, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.19→59.14 Å / Num. obs: 29641 / % possible obs: 80.3 % / Redundancy: 25.8 % / Biso Wilson estimate: 94.06 Å2 / Rsym value: 0.129 / Net I/σ(I): 19
Reflection shellResolution: 3.19→3.27 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.56 / Rsym value: 0.476 / % possible all: 21.4

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
SAWAYAANISOTROPY SERVERdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3RYC, 2P4N, 2XEE

3ryc

2p4n

2xee


Resolution: 3.19→59.14 Å / Cor.coef. Fo:Fc: 0.9004 / Cor.coef. Fo:Fc free: 0.8708 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BEFORE REFINEMENT, THE REFLECTION DATA WERE ANISOTROPICALLY SCALED AND TRUNCATED USING THE ANISOTROPY SERVER AT HTTP://SERVICES.MBI.UCLA.EDU/ANISOSCALE/
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1519 5.12 %RANDOM
Rwork0.1767 ---
obs0.1784 29641 80.25 %-
Displacement parametersBiso mean: 80.26 Å2
Baniso -1Baniso -2Baniso -3
1--15.3645 Å20 Å20 Å2
2--5.305 Å20 Å2
3---10.0595 Å2
Refine analyzeLuzzati coordinate error obs: 0.656 Å
Refinement stepCycle: LAST / Resolution: 3.19→59.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10505 0 100 2 10607
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110811HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2314660HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3763SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes297HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1603HARMONIC5
X-RAY DIFFRACTIONt_it10811HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion20.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1427SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12228SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.3 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3416 39 4.56 %
Rwork0.2246 817 -
all0.2293 856 -
obs--80.25 %
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)
11.6650.2009-0.98893.7782-0.88793.3673-0.0114-0.382-0.24810.64720.00580.5170.03380.01630.00560.0256-0.07060.304-0.06410.0614-0.057-4.69342.385338.2622
21.27590.50280.12132.5439-0.95042.5562-0.05930.03290.0939-0.37150.10010.5085-0.089-0.3304-0.04080.06120.00510.081-0.0234-0.07520.0624-5.60659.4465-0.1471
33.85942.13911.25848.93521.67095.656-0.01330.2682-0.14280.14780.0480.3160.2501-0.4047-0.03470.066-0.073-0.03910.03260.0931-0.22225.377571.6902-31.922
41.84310.35350.42232.7785-0.23264.07530.07830.0180.0691-0.0303-0.07130.0629-0.14380.1825-0.0071-0.175-0.14730.1699-0.3268-0.1012-0.334419.196583.906724.1645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 601
2X-RAY DIFFRACTION2{ B|* }B1 - 650
3X-RAY DIFFRACTION3{ D|* }D11 - 169
4X-RAY DIFFRACTION4{ K|* }K4 - 650

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