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- EMDB-64322: Giraffe KIF5A motor domain in nucleotide free state bound to micr... -

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Basic information

Entry
Database: EMDB / ID: EMD-64322
TitleGiraffe KIF5A motor domain in nucleotide free state bound to microtubule
Map data
Sample
  • Complex: gcKIF5A is attached to microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: GcKIF5A
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsGiraffe Kinesin motor KIF Microtubule / MOTOR PROTEIN
Function / homology
Function and homology information


Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / odontoblast differentiation / Neutrophil degranulation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion ...Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / odontoblast differentiation / Neutrophil degranulation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / nuclear envelope lumen / regulation of synapse organization / MHC class I protein binding / intercellular bridge / spindle assembly / structural constituent of cytoskeleton / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / mitotic spindle / mitotic cell cycle / microtubule cytoskeleton / cell body / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1B chain / Tubulin beta chain
Similarity search - Component
Biological speciesGiraffa camelopardalis (giraffe) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsImasaki T / Yamagishi Y / Shigematsu H / Nitta R
Funding support Japan, 1 items
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 23, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64322.png

Downloads & links

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Map

FileDownload / File: emd_64322.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 400 pix.
= 596. Å		1.49 Å/pix.
x 400 pix.
= 596. Å		1.49 Å/pix.
x 400 pix.
= 596. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.009321059 - 0.036877435
Average (Standard dev.)0.00029371085 (±0.004843026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 596.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Postprocessed map. Model was built using this map.

Fileemd_64322_additional_1.map
AnnotationPostprocessed map. Model was built using this map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64322_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64322_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : gcKIF5A is attached to microtubule

EntireName: gcKIF5A is attached to microtubule
Components
  • Complex: gcKIF5A is attached to microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: GcKIF5A
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: gcKIF5A is attached to microtubule

SupramoleculeName: gcKIF5A is attached to microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Giraffa camelopardalis (giraffe)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.574766 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDD SFNTFFSETG AGKHVPRAVF VDLEPTVIDE VRTGTYRQLF HPEQLITGK EDAANNYARG HYTIGKEIID LVLDRIRKLA DQCTGLQGFL VFHSFGGGTG SGFTSLLMER LSVDYGKKSK L EFSIYPAP ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDD SFNTFFSETG AGKHVPRAVF VDLEPTVIDE VRTGTYRQLF HPEQLITGK EDAANNYARG HYTIGKEIID LVLDRIRKLA DQCTGLQGFL VFHSFGGGTG SGFTSLLMER LSVDYGKKSK L EFSIYPAP QVSTAVVEPY NSILTTHTTL EHSDCAFMVD NEAIYDICRR NLDIERPTYT NLNRLISQIV SSITASLRFD GA LNVDLTE FQTNLVPYPR IHFPLATYAP VISAEKAYHE QLSVAEITNA CFEPANQMVK CDPRHGKYMA CCLLYRGDVV PKD VNAAIA TIKTKRSIQF VDWCPTGFKV GINYQPPTVV PGGDLAKVQR AVCMLSNTTA IAEAWARLDH KFDLMYAKRA FVHW YVGEG MEEGEFSEAR EDMAALEKDY EEVGVDSVEG EGEEEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.717629 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQVFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAVT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEED FGEEAEEEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: GcKIF5A

MacromoleculeName: GcKIF5A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Giraffa camelopardalis (giraffe)
Molecular weightTheoretical: 37.340449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE QVYHACAMQI VKDVLAGYNG TIFAYGQTS SGKTHTMEGK LHDPQLMGII PRIVQDIFNH IYSMDENLEF HIKVSYFEIY LDKIRDLLDV TKTNLAVHED K NRVPFVKG ...String:
MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE QVYHACAMQI VKDVLAGYNG TIFAYGQTS SGKTHTMEGK LHDPQLMGII PRIVQDIFNH IYSMDENLEF HIKVSYFEIY LDKIRDLLDV TKTNLAVHED K NRVPFVKG CTERFVSSPE EILDVIDEGK SNRHVAVTNM NEHSSRSHSI FLINIKQENM ETEQKLSGKL YLVDLAGSEK VS KTGAEGA VLDEAKNINK SLSALGNVIS ALAEGTKSYV PYRDSKMTRI LQDSLGGNCR TTMFICCSPS SFNDAETKST LMF GQRAKT IKNTASVN

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration4 mg/mL
BufferpH: 6.9
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 310 K

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.8 °
Applied symmetry - Helical parameters - Axial symmetry: C14 (14 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28333
CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

6353

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9umm


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9umu:
Giraffe KIF5A motor domain in nucleotide free state bound to microtubule

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