9yai

KIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP

Method: ELECTRON MICROSCOPY Dmax: 188.3 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Kinesin-like protein KIF1A

Homo sapiens

UniProt Q12756

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain K; UniProt 1–393 Chain N; UniProt 1–393 Mutation:R350W Tubulin alpha-1B chain × 2 (Q2XVP4) Tubulin beta-2B chain × 2 (A0A287AGU7) MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane. Resolution 3.12 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

20 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KIF1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain K; PDBConstruct 1–393; UniProt 1–393 Author chain N; PDBConstruct 1–393; UniProt 1–393

Tubulin alpha-1B chain

OrganismNot specified

UniProt Q2XVP4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–451 Chain E; UniProt 1–451 Not recorded Kinesin-like protein KIF1A × 2 (Q12756) Tubulin beta-2B chain × 2 (A0A287AGU7) MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane. Resolution 3.12 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

230 other PDB entries and 243 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_PIG
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451 Author chain E; PDBConstruct 1–451; UniProt 1–451

Tubulin beta-2B chain

OrganismNot specified

UniProt A0A287AGU7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–445 Chain I; UniProt 1–445 Not recorded Kinesin-like protein KIF1A × 2 (Q12756) Tubulin alpha-1B chain × 2 (Q2XVP4) MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane. Resolution 3.12 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

98 other PDB entries and 98 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A287AGU7_PIG
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 1–445; UniProt 1–445 Author chain I; PDBConstruct 1–445; UniProt 1–445

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9yai

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yai
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yai
Deposition date deposition_date2025-09-16
Structure title titleKIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP
Keywords keywordsKIF1A, Kinesin-3 superfamily, KIF1A R350W mutant, motor domain, AMP-PNP bound, cargo transport, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.47
Radius of gyration Rg (electron density) rg_electron52.78
Forward intensity I(0) i01220180000.00
Molecular weight molecular_weight281670.0 kDa
Excluded volume excluded_volume348290 ų
Envelope volume envelope_volume465500 ų
Hydration-shell volume shell_volume76374 ų
Envelope diameter envelope_diameter194.0
Shell Rg shell_rg52.32
Envelope Rg envelope_rg52.44
Shape Rg shape_rg52.78
Total Rg total_rg52.74
Total atoms total_atoms19749
Residues n_residues2478
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax188.3
Rg (real space) rg_real52.82
Rg uncertainty (real space) rg_real_error2.70
I(0) (real space) i0_real1.2200e+09
I(0) uncertainty (real space) i0_real_error2.7060e+07
Rg (reciprocal space) rg_reciprocal52.17
I(0) (reciprocal space) i0_reciprocal1219000000.0000
Solution quality estimate total_estimate0.8252
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.2
Skewness Skewness skewness0.505
Kurtosis Kurtosis kurtosis-0.414
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha154600000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.679; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.783

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)