8utr

KIF1A[1-393] ADP bound in complex with a microtubule

Method: ELECTRON MICROSCOPY Dmax: 114.8 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 1–393 Fragment:residues 1-393 Tubulin alpha-1B chain × 1 (Q2XVP4) Tubulin beta-2B chain × 1 (A0A287AGU7) ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–451 Not recorded Kinesin-like protein KIF1A × 1 (Q12756) Tubulin beta-2B chain × 1 (A0A287AGU7) ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–445 Not recorded Kinesin-like protein KIF1A × 1 (Q12756) Tubulin alpha-1B chain × 1 (Q2XVP4) ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 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

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 8utr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8utr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8utr
Deposition date deposition_date2023-10-31
Structure title titleKIF1A[1-393] ADP bound in complex with a microtubule
Keywords keywordsKIF1A, kinesin, motility, microtubule, tubulin, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.27
Radius of gyration Rg (electron density) rg_electron33.51
Forward intensity I(0) i0321108000.00
Molecular weight molecular_weight139670.0 kDa
Excluded volume excluded_volume172730 ų
Envelope volume envelope_volume221730 ų
Hydration-shell volume shell_volume53530 ų
Envelope diameter envelope_diameter124.3
Shell Rg shell_rg41.48
Envelope Rg envelope_rg33.73
Shape Rg shape_rg33.52
Total Rg total_rg34.03
Total atoms total_atoms9792
Residues n_residues1230
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 dmax114.8
Rg (real space) rg_real34.19
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real3.2110e+08
I(0) uncertainty (real space) i0_real_error5.5530e+06
Rg (reciprocal space) rg_reciprocal34.24
I(0) (reciprocal space) i0_reciprocal321100000.0000
Solution quality estimate total_estimate0.8841
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.9
Skewness Skewness skewness0.277
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha94580000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)