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- PDB-5nfd: Antiparallel monomeric coiled coil of Kif21A -

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Basic information

Entry
Database: PDB / ID: 5nfd
TitleAntiparallel monomeric coiled coil of Kif21A
ComponentsKinesin-like protein KIF21A
KeywordsMOTOR PROTEIN / coiled coil / kinesin
Function / homology
Function and homology information


ankyrin repeat binding / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / microtubule-based movement / microtubule binding / microtubule / axon / dendrite ...ankyrin repeat binding / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / microtubule-based movement / microtubule binding / microtubule / axon / dendrite / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF21A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å
AuthorsKraatz, S.H.W. / Bianchi, S. / Steinmetz, M.O.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Biosci. Rep. / Year: 2018
Title: Combinatorial use of disulfide bridges and native sulfur-SAD phasing for rapid structure determination of coiled-coils.
Authors: Kraatz, S.H.W. / Bianchi, S. / Steinmetz, M.O.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF21A
B: Kinesin-like protein KIF21A


Theoretical massNumber of molelcules
Total (without water)18,9292
Polymers18,9292
Non-polymers00
Water1,802100
1
A: Kinesin-like protein KIF21A


Theoretical massNumber of molelcules
Total (without water)9,4651
Polymers9,4651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF21A


Theoretical massNumber of molelcules
Total (without water)9,4651
Polymers9,4651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.970, 41.670, 123.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinesin-like protein KIF21A / Kinesin-like protein KIF2 / Renal carcinoma antigen NY-REN-62


Mass: 9464.645 Da / Num. of mol.: 2 / Fragment: UNP residues 938-1017
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF21A, KIAA1708, KIF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7Z4S6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.0, 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0664 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.18→41.68 Å / Num. obs: 8779 / % possible obs: 90 % / Redundancy: 9.6 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 54.6
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 9.6 / Num. unique all: 336 / CC1/2: 0.987 / % possible all: 35

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Processing

Software
NameVersionClassification
PHENIXdev_1965refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.18→39.498 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 24.25
RfactorNum. reflection% reflection
Rfree0.2392 1554 10.07 %
Rwork0.1973 --
obs0.2015 8778 86.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→39.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 0 100 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021246
X-RAY DIFFRACTIONf_angle_d0.4261657
X-RAY DIFFRACTIONf_dihedral_angle_d10.764525
X-RAY DIFFRACTIONf_chiral_restr0.025185
X-RAY DIFFRACTIONf_plane_restr0.001222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1762-2.24640.2196370.222314X-RAY DIFFRACTION21
2.2464-2.32670.238970.2216797X-RAY DIFFRACTION57
2.3267-2.41980.26681360.20231158X-RAY DIFFRACTION80
2.4198-2.52990.24531490.20251391X-RAY DIFFRACTION96
2.5299-2.66330.24911690.21621465X-RAY DIFFRACTION100
2.6633-2.83010.25931670.20671484X-RAY DIFFRACTION100
2.8301-3.04850.30241580.20841429X-RAY DIFFRACTION100
3.0485-3.35520.25281630.22141479X-RAY DIFFRACTION100
3.3552-3.84030.21191560.17261466X-RAY DIFFRACTION100
3.8403-4.8370.20121670.17241445X-RAY DIFFRACTION100
4.837-39.50420.23781550.20151457X-RAY DIFFRACTION100

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