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9w9i

Cryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC

Method: ELECTRON MICROSCOPY Dmax: 142.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Kinesin-like protein KIF3A

Mus musculus

UniProt P28741

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 536–701 Not recorded Kinesin-like protein KIF3B, N-terminally processed × 1 （Q61771） Kinesin-associated protein 3 × 1 （P70188） Adenomatous polyposis coli protein × 1 （Q61315） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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.

Other PDB Difference from Current Entry 9W9I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5JVR The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix of Drosophila melanogaster Kinesin-1 fused to EB1 Deposited 2016-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Chain B 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；32% (w/v) polyethylene glycol dimethyl ether (DMPEG) 500, 30 mM MgCl2, 10 mM diethylenetriamine, 100 mM sodium 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) pH 8.5
Resolution 2.10 Å R-free 0.234
5JVR The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix of Drosophila melanogaster Kinesin-1 fused to EB1 Deposited 2016-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Chain D 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；32% (w/v) polyethylene glycol dimethyl ether (DMPEG) 500, 30 mM MgCl2, 10 mM diethylenetriamine, 100 mM sodium 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) pH 8.5
Resolution 2.10 Å R-free 0.234
5JVR The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix of Drosophila melanogaster Kinesin-1 fused to EB1 Deposited 2016-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Chain F 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；32% (w/v) polyethylene glycol dimethyl ether (DMPEG) 500, 30 mM MgCl2, 10 mM diethylenetriamine, 100 mM sodium 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) pH 8.5
Resolution 2.10 Å R-free 0.234
5JVR The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix of Drosophila melanogaster Kinesin-1 fused to EB1 Deposited 2016-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Chain H 352–359（8 aa） Fragment：UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；32% (w/v) polyethylene glycol dimethyl ether (DMPEG) 500, 30 mM MgCl2, 10 mM diethylenetriamine, 100 mM sodium 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) pH 8.5
Resolution 2.10 Å R-free 0.234
5JX1 The neck-linker and alpha 7 helix of Mus musculus KIF3A fused to EB1 Deposited 2016-05-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 352–376（25 aa） Fragment：UNP P28741 residues 352-376,UNP Q15691 residues 210-257
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；24% (w/v) 2-methyl-2,4-pentanediol (MPD), 10% (w/v) PEG 4000, 100 mM CaCl2, 100 mM (3-(N-morpholino)propanesulfonic acid) (MOPS) pH 7.0, 1 mM CdCl2
Resolution 1.67 Å R-free 0.228
9W9H Cryo-EM structure of the mouse kinesin-2 tail in complex with KAP3 adaptor Deposited 2025-08-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 481–701（221 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KIF3A_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 13–178； UniProt 536–701

Kinesin-like protein KIF3B, N-terminally processed

Mus musculus

UniProt Q61771

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 529–747 Not recorded Kinesin-like protein KIF3A × 1 （P28741） Kinesin-associated protein 3 × 1 （P70188） Adenomatous polyposis coli protein × 1 （Q61315） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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.

Other PDB Difference from Current Entry 9W9I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9W9H Cryo-EM structure of the mouse kinesin-2 tail in complex with KAP3 adaptor Deposited 2025-08-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 475–747（273 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KIF3B_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–220； UniProt 529–747

Kinesin-associated protein 3

Mus musculus

UniProt P70188

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–693 Not recorded Kinesin-like protein KIF3A × 1 （P28741） Kinesin-like protein KIF3B, N-terminally processed × 1 （Q61771） Adenomatous polyposis coli protein × 1 （Q61315） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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.

Other PDB Difference from Current Entry 9W9I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9W9H Cryo-EM structure of the mouse kinesin-2 tail in complex with KAP3 adaptor Deposited 2025-08-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–693（693 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KIFA3_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–693； UniProt 1–693

Adenomatous polyposis coli protein

Mus musculus

UniProt Q61315

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 338–1010 Not recorded Kinesin-like protein KIF3A × 1 （P28741） Kinesin-like protein KIF3B, N-terminally processed × 1 （Q61771） Kinesin-associated protein 3 × 1 （P70188） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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.

Other PDB Difference from Current Entry 9W9I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1VJ6 PDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein Deposited 2004-02-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2834–2845（12 aa） Fragment：C-terminus of APC
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1mM PDZ2 protein, U-15N,13C; 3mM APC peptide, unlabelled | 50 mM KH2PO4/K2HPO4 50 mM KCl, pH 6.8, H2O/D2O (95%/5%)
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APC_MOUSE
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 8–680； UniProt 338–1010

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 9w9i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9w9i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9w9i
Deposition date deposition_date2025-08-10
Structure title titleCryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC
Keywords keywordsKinesin-2 motor Intracellular transport Kinesin-adaptor-cargo complex, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.61 Å
Radius of gyration Rg (electron density) rg_electron44.23 Å
Forward intensity I(0) i0179389000.00
Molecular weight molecular_weight109990.0 kDa
Excluded volume excluded_volume137900 ų
Envelope volume envelope_volume214530 ų
Hydration-shell volume shell_volume40837 ų
Envelope diameter envelope_diameter146.7 Å
Shell Rg shell_rg49.13 Å
Envelope Rg envelope_rg42.62 Å
Shape Rg shape_rg44.27 Å
Total Rg total_rg44.33 Å
Total atoms total_atoms7711
Residues n_residues1011
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax142.3 Å
Rg (real space) rg_real44.66 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real1.7940e+08
I(0) uncertainty (real space) i0_real_error2.9620e+06
Rg (reciprocal space) rg_reciprocal44.61 Å
I(0) (reciprocal space) i0_reciprocal179400000.0000
Solution quality estimate total_estimate0.8482
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.119
Kurtosis Kurtosis kurtosis-0.903
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8372000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.813; Smooth: 0.720
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)