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- PDB-5d3a: KIF21A regulatory coiled coil -

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Basic information

Entry
Database: PDB / ID: 5d3a
TitleKIF21A regulatory coiled coil
ComponentsKinesin-like protein KIF21A
KeywordsMOTOR PROTEIN / antiparallel / coiled coil / kinesin / autoinhibition
Function / homology
Function and homology information


regulation of microtubule depolymerization / regulation of axon guidance / cortical microtubule organization / ankyrin repeat binding / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement ...regulation of microtubule depolymerization / regulation of axon guidance / cortical microtubule organization / ankyrin repeat binding / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement / regulation of microtubule polymerization / axonal growth cone / microtubule binding / microtubule / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsBianchi, S. / Kraatz, S. / Steinmetz, M.O. / Kammerer, A.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Switzerland
CitationJournal: To Be Published
Title: Structure of KIF21A regulatory coiled coil
Authors: Bianchi, S. / Kraatz, S. / Steinmetz, M.O. / Kammerer, A.R.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1704
Polymers18,9852
Non-polymers1842
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-42 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.020, 82.020, 70.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 9492.697 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M citric acid, 10 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.06641 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.06641 Å / Relative weight: 1
ReflectionResolution: 2.495→71.03 Å / Num. obs: 9871 / % possible obs: 99.95 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.1762 / Net I/σ(I): 15.84
Reflection shellResolution: 2.495→2.584 Å / Rmerge(I) obs: 1.785

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Processing

Software
NameVersionClassification
PHENIXdev_1965refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.495→71.03 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2023 921 4.98 %
Rwork0.1753 --
obs0.1785 18494 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.495→71.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 12 7 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021322
X-RAY DIFFRACTIONf_angle_d0.4651752
X-RAY DIFFRACTIONf_dihedral_angle_d13.307552
X-RAY DIFFRACTIONf_chiral_restr0.03192
X-RAY DIFFRACTIONf_plane_restr0.001236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4969-2.62840.33641300.25812521X-RAY DIFFRACTION95
2.6284-2.79280.30221310.24572487X-RAY DIFFRACTION95
2.7928-3.0080.28631340.20352515X-RAY DIFFRACTION95
3.008-3.30980.21831300.19482506X-RAY DIFFRACTION95
3.3098-3.78680.17691300.15112502X-RAY DIFFRACTION95
3.7868-4.76340.15831350.14672483X-RAY DIFFRACTION95
4.7634-22.44830.18711300.17172518X-RAY DIFFRACTION95

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