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- PDB-7d8v: Crystal Structure of A Kinesin-3 KIF13B mutant-T192Y -

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Basic information

Entry
Database: PDB / ID: 7d8v
TitleCrystal Structure of A Kinesin-3 KIF13B mutant-T192Y
ComponentsKinesin family member 13BKinesin-like protein KIF13B
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 / kinesin complex / microtubule motor activity / 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 / kinesin complex / microtubule motor activity / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding / microtubule binding / microtubule / axon / protein kinase binding / ATP hydrolysis activity / ATP 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 / 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 / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
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 / molecular replacement / Resolution: 2.3 Å
AuthorsRen, J.Q. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plos Genet. / Year: 2021
Title: Motor domain-mediated autoinhibition dictates axonal transport by the kinesin UNC-104/KIF1A.
Authors: Cong, D.Z. / Ren, J.Q. / Zhou, Y.R. / Wang, S. / Liang, J.J. / Ding, M. / Feng, W.
History
DepositionOct 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6664
Polymers49,0921
Non-polymers5743
Water2,036113
1
A: Kinesin family member 13B
hetero molecules

A: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3328
Polymers98,1852
Non-polymers1,1476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area4720 Å2
ΔGint-32 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.510, 87.510, 97.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

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Components

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


Mass: 49092.367 Da / Num. of mol.: 1 / Mutation: T192Y
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 0.1M Bis-Tris propane, 30% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→32.56 Å / Num. obs: 19638 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 40.537 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 961 / CC1/2: 0.725 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A1Z

6a1z


Resolution: 2.3→29.92 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 986 5.03 %
Rwork0.182 18622 -
obs0.1848 19608 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.96 Å2 / Biso mean: 50.9832 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 2.3→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 36 113 2960
Biso mean--45.43 48.7 -
Num. residues----365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.420.27171370.228526162753
2.42-2.570.30771800.213326022782
2.57-2.770.25631320.204526092741
2.77-3.050.28221380.195726552793
3.05-3.490.26721240.181926562780
3.49-4.390.21581550.160726742829
4.4-29.920.211200.175228102930
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)
15.5775-1.1293-0.47482.56460.52813.02690.1645-0.09830.27370.0225-0.0891-0.0804-0.43380.0096-0.0910.3585-0.03910.03010.2848-0.06510.342-33.568927.66590.463
21.7372-0.5794-0.72461.35580.37114.58510.1798-0.0660.0135-0.1231-0.0963-0.0952-0.13690.2449-0.09690.2275-0.0394-0.01260.2584-0.010.2822-30.766111.2326-19.2943
30.1169-0.00460.61261.44450.13943.00380.0387-0.1791-0.04960.12890.03650.09510.0829-0.1867-0.07950.27890.00290.00150.358-0.00730.3607-26.82594.5258-13.8776
42.5728-1.2056-2.14770.95130.88831.3270.072-0.16030.2292-0.01610.1257-0.3096-0.00630.1682-0.19660.27940.0074-0.01560.453-0.07040.3252-13.521110.0221-12.319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 75 )A3 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 171 )A76 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 304 )A172 - 304
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 384 )A305 - 384

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