2hxf

KIF1A head-microtubule complex structure in amppnp-form

Method: ELECTRON MICROSCOPY Dmax: 113.9 Å Quality: GOOD

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

Tubulin alpha chain

OrganismNot specified

UniProt P02550

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 Tubulin beta chain × 1 (P02554) Kinesin-like protein KIF1A × 1 (P33173) MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer:IMIDAZOLE;pH 7.4;IMIDAZOLE cryo-EM vitrification conditions:Ethan slash Resolution 10.00 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.

39 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

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

Tubulin beta chain

OrganismNot specified

UniProt P02554

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 Tubulin alpha chain × 1 (P02550) Kinesin-like protein KIF1A × 1 (P33173) MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer:IMIDAZOLE;pH 7.4;IMIDAZOLE cryo-EM vitrification conditions:Ethan slash Resolution 10.00 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.

137 other PDB entries and 159 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB_PIG
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–435; UniProt 1–445

Kinesin-like protein KIF1A

Mus musculus

UniProt P33173

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 C; UniProt 1–355 Fragment:KIF1A HEAD DOMAIN Mutation:P202A Tubulin alpha chain × 1 (P02550) Tubulin beta chain × 1 (P02554) MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer:IMIDAZOLE;pH 7.4;IMIDAZOLE cryo-EM vitrification conditions:Ethan slash Resolution 10.00 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.

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KIF1A_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 19–371; UniProt 1–355

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 2hxf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hxf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hxf
Deposition date deposition_date2006-08-03
Structure title titleKIF1A head-microtubule complex structure in amppnp-form
Keywords keywordsmicrotubule-based motor, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.22
Radius of gyration Rg (electron density) rg_electron32.50
Forward intensity I(0) i0287646000.00
Molecular weight molecular_weight132280.0 kDa
Excluded volume excluded_volume163680 ų
Envelope volume envelope_volume197930 ų
Hydration-shell volume shell_volume49296 ų
Envelope diameter envelope_diameter120.6
Shell Rg shell_rg40.38
Envelope Rg envelope_rg32.88
Shape Rg shape_rg32.51
Total Rg total_rg33.03
Total atoms total_atoms9279
Residues n_residues1162
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 dmax113.9
Rg (real space) rg_real33.14
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real2.8760e+08
I(0) uncertainty (real space) i0_real_error4.8320e+06
Rg (reciprocal space) rg_reciprocal33.18
I(0) (reciprocal space) i0_reciprocal287700000.0000
Solution quality estimate total_estimate0.8780
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.0
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.359
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha95970000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2hxfa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd2hxfa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd2hxfb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd2hxfb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd2hxfc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.9 — Motor proteins

8. Citations (1)

9. Files and Curves (10)