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- PDB-6a20: Crystal Structure of auto-inhibited Kinesin-3 KIF13B -

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Basic information

Entry
Database: PDB / ID: 6a20
TitleCrystal Structure of auto-inhibited Kinesin-3 KIF13B
ComponentsKinesin family member 13B
KeywordsTRANSPORT PROTEIN / kinesin / ATPase
Function / homology
Function and homology information


Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / paranode region of axon / microtubule motor activity / kinesin complex / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding ...Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / paranode region of axon / microtubule motor activity / kinesin complex / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding / microtubule binding / microtubule / axon / protein kinase binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY ...Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Kinesin-associated / Kinesin-associated / Kinesin motor domain / Kinesin / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin family member 13B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRen, J.Q. / Wang, S. / Feng, W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Coiled-coil 1-mediated fastening of the neck and motor domains for kinesin-3 autoinhibition.
Authors: Ren, J.Q. / Wang, S. / Chen, H. / Wang, W.J. / Huo, L. / Feng, W.
History
DepositionJun 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7285
Polymers48,9701
Non-polymers7584
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-25 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.070, 75.070, 91.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Kinesin family member 13B / Kinesin-3 KIF13B


Mass: 48970.270 Da / Num. of mol.: 1 / Mutation: Y73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kif13b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2K8Z9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.31 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5
Details: 0.2M proline, 0.1M HEPES, pH 7.5, 14% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22223 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.615 / Num. unique obs: 3271

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZBS

5zbs


Resolution: 2.4→30.639 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.2488 1155 5.2 %
Rwork0.1934 --
obs0.1962 22215 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→30.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 48 195 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023193
X-RAY DIFFRACTIONf_angle_d0.6024314
X-RAY DIFFRACTIONf_dihedral_angle_d13.5191191
X-RAY DIFFRACTIONf_chiral_restr0.023498
X-RAY DIFFRACTIONf_plane_restr0.002551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.50950.3471440.27682655X-RAY DIFFRACTION99
2.5095-2.64170.31211400.26112640X-RAY DIFFRACTION99
2.6417-2.80710.30121440.2462654X-RAY DIFFRACTION99
2.8071-3.02370.28421520.23122626X-RAY DIFFRACTION99
3.0237-3.32760.29071460.2182642X-RAY DIFFRACTION99
3.3276-3.80840.26321520.18012654X-RAY DIFFRACTION99
3.8084-4.79520.21141350.15892547X-RAY DIFFRACTION96
4.7952-30.64110.1921420.16412642X-RAY DIFFRACTION98
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)
12.66330.6345-0.81171.5128-0.52711.78650.08680.12960.23370.17710.02610.197-0.3572-0.1691-0.12670.4550.0172-0.02760.31310.06940.39932.63818.3117-3.7046
22.64740.26530.20261.68671.35964.46410.02360.1296-0.16460.17510.0746-0.19660.0980.5824-0.07350.3198-0.0101-0.05450.35490.07870.415223.00931.6915-8.1358
33.1020.0793-0.61410.25670.24191.4971-0.02890.0145-0.04950.23220.0216-0.16980.02250.5583-0.030.4841-0.0147-0.04660.50020.07680.484629.36555.8371-7.9807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 433 )

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