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- PDB-9umn: Giraffe KIF5A motor domain crystallized in the presence of 1 mM AMPPNP -

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Basic information

Entry
Database: PDB / ID: 9umn
TitleGiraffe KIF5A motor domain crystallized in the presence of 1 mM AMPPNP
ComponentsGcKIF5A
KeywordsMOTOR PROTEIN / Giraffe Kinesin motor KIF
Function / homologyACETATE ION
Function and homology information
Biological speciesGiraffa camelopardalis (giraffe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsImasaki, T. / Sakai, N. / Nitta, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJFR214K Japan
CitationJournal: To Be Published
Title: Enhanced Axonal Transport in Large Vertebrates: KIF5A Adaptations in Giraffes and Pythons
Authors: Kambara, T. / Rao, L. / Yamagishi, Y. / Ikeda, K. / Taniguchi, D. / Imasaki, T. / Shigematsu, H. / Sakai, N. / Gennerich, A. / Nitta, R. / Okada, Y.
History
DepositionApr 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GcKIF5A
B: GcKIF5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1758
Polymers74,6812
Non-polymers4946
Water9,836546
1
A: GcKIF5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5884
Polymers37,3401
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area14000 Å2
MethodPISA
2
B: GcKIF5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5884
Polymers37,3401
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.060, 51.060, 77.140
Angle α, β, γ (deg.)100.390, 108.060, 93.300
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein GcKIF5A


Mass: 37340.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Because sequence of gcKIF5A is not depositted to the database, we could not list ID. Here is the full-length sequence >gcKIF5A ...Details: Because sequence of gcKIF5A is not depositted to the database, we could not list ID. Here is the full-length sequence >gcKIF5A MAETNNECSIKVLCRFRPLNQAEILRGDKFIPIFQGDDSVVIGGKPYVFDRVFPPNTTQEQVYHACAMQIVKDVLAGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIAQDIFNHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVTKTNLAVHEDKNRVPFVKGCTERFVSSPEEILDVIDEGKSNRHVAVTNMNEHSSRSHSIFLINIKQENMETEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGTKSYVPYRDSKMTRILQDSLGGNCRTTMFICCSPSSFNDAETKSTLMFGQRAKTIKNTASVNLELTAEQWKKKYEKEKEKTKAQKETIAKLEAELSRWRNGENVPETERLAGEDAALGAELCEETPVNDNSSIVVRIAPEERQKYEEEIRRLYKQLDDKDDEINQQSQLIEKLKQQMLDQEELLVSTRGDNEKVQRELSHLQSENDAAKDEVKEVLQALEELAMNYDQKSQEVEEKSQQNQLLVDELSQKVATMLSLESELQRLQEVSGHQRKRIAEVLNGLMKDLSEFSVIVGNGEIKLPVEISGAIEEEFTVARLYISKIKSEVKSVVKRCRQLENLQVECHRKMEVTGRELSSCQLLISQHEAKIRSLTEYMQSVELKKRHLEESYDSLSDELAKLQAQETVHEVALKDKEPDTQDTEDVKASGESKALEVQMENHREAHHRQLARLRDEINEKQKTIDELKDLNQKLQLELEKLQADYEKLKNEEHEKSTKLQELTFLYERHEQSKQDLKGLEETVARELQTLHNLRKLFVQDVTTRVKKSAEMEPEDSGGIHSQKQKISFLENNLEQLTKVHKQLVRDNADLRCELPKLEKRLRATAERVKALEGALKEAKEGAMKDKRRYQQEVDRIKEAVRYKSSGKRGHSAQIAKPVRPGHYPASSPTNPYGTRSPECISYTNSLFQNYQNLYLQAAPSSTSDMYFPNSCTSSGATSSGGPLTSYQKANMDNGNATDINDNRSDLPCGYEAEDQAKLFPLHQETAAS
Source: (gene. exp.) Giraffa camelopardalis (giraffe) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8-2.0 M ammonium sulfate 0.2-0.5 M di-ammonium tartrate 0.1 M sodium acetate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 60002 / % possible obs: 96.9 % / Redundancy: 3.55 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.083 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 34941 / CC1/2: 0.861 / Rrim(I) all: 0.565

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Processing

Software
NameVersionClassification
PHENIXv2.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→45.64 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.2112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 3001 5 %
Rwork0.1972 57001 -
obs0.1993 60002 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.75 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 30 546 5341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634887
X-RAY DIFFRACTIONf_angle_d0.84456582
X-RAY DIFFRACTIONf_chiral_restr0.0533741
X-RAY DIFFRACTIONf_plane_restr0.0062847
X-RAY DIFFRACTIONf_dihedral_angle_d15.56071833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.33341360.29042588X-RAY DIFFRACTION92.03
1.88-1.910.28251400.26412651X-RAY DIFFRACTION95.75
1.91-1.950.28541430.24292714X-RAY DIFFRACTION95.49
1.95-1.980.3111400.22892663X-RAY DIFFRACTION96.76
1.98-2.020.29091420.2172711X-RAY DIFFRACTION96.42
2.02-2.070.2491420.20542683X-RAY DIFFRACTION96.06
2.07-2.120.22351440.20512744X-RAY DIFFRACTION96.91
2.12-2.170.26861410.19532672X-RAY DIFFRACTION97.03
2.17-2.230.25411440.20012745X-RAY DIFFRACTION96.75
2.23-2.290.26041410.2032669X-RAY DIFFRACTION97.1
2.29-2.370.26481420.20952710X-RAY DIFFRACTION97.21
2.37-2.450.28731440.20352737X-RAY DIFFRACTION97.46
2.45-2.550.24921460.2082770X-RAY DIFFRACTION97.46
2.55-2.670.2591430.19662716X-RAY DIFFRACTION97.84
2.67-2.810.23611440.20832732X-RAY DIFFRACTION97.92
2.81-2.980.31181460.20042767X-RAY DIFFRACTION98.31
2.98-3.210.22491440.19792737X-RAY DIFFRACTION97.86
3.21-3.540.22641430.17882716X-RAY DIFFRACTION97.88
3.54-4.050.19281440.17092740X-RAY DIFFRACTION98.13
4.05-5.10.19181460.16412770X-RAY DIFFRACTION98.38
5.1-45.640.22851460.21542766X-RAY DIFFRACTION99.28

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