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3lre

Crystal Structure Analysis of Human Kinesin-8 Motor Domain

Method: X-RAY DIFFRACTION Dmax: 96.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Kinesin-like protein KIF18A

Homo sapiens

UniProt Q8NI77

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–355 Fragment：UNP residues 1-355 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.8；275 K；10-13% PEG 20000, 0.1M HEPES pH 7.8, 2% dioxane, vapor diffusion, temperature 275K Resolution 2.20 Å R-free 0.277
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–355 Fragment：UNP residues 1-355 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.8；275 K；10-13% PEG 20000, 0.1M HEPES pH 7.8, 2% dioxane, vapor diffusion, temperature 275K Resolution 2.20 Å R-free 0.277
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–355 Chain B； UniProt 1–355 Fragment：UNP residues 1-355 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.8；275 K；10-13% PEG 20000, 0.1M HEPES pH 7.8, 2% dioxane, vapor diffusion, temperature 275K Resolution 2.20 Å R-free 0.277

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 3LRE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5OAM Molecular basis of human kinesin-8 function and inhibition Deposited 2017-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–374（374 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
5OCU Molecular basis of human kinesin-8 function and inhibition Deposited 2017-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–374（374 aa）
Not recorded MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
5OGC Molecular basis of human kinesin-8 function and inhibition Deposited 2017-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–374（374 aa）
Not recorded 9V5 4-chloranyl-2-nitro-1-(phenylsulfonyl)benzene × 1 ZN ZINC ION × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7RSI The cryo-EM map of KIF18A bound to KIFBP Deposited 2021-08-11 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 C 1–353（353 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9DI0 Cryo-EM structure of Kif18A bound to a microtubule Deposited 2024-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–374（373 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 TA1 TAXOL × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9YMG Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–367（367 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M ammonium nitrate, 0.1 M sodium acetate pH 5.6, 20% (w/v) PEG Smear Low (5% PEG 400, 5% PEG 500 MME, 5% PEG 600, 5% PEG 1000), 5% (v/v) ethylene glycol
Resolution 2.41 Å R-free 0.238
9YMG Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin Deposited 2025-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–367（367 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M ammonium nitrate, 0.1 M sodium acetate pH 5.6, 20% (w/v) PEG Smear Low (5% PEG 400, 5% PEG 500 MME, 5% PEG 600, 5% PEG 1000), 5% (v/v) ethylene glycol
Resolution 2.41 Å R-free 0.238

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KI18A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–355； UniProt 1–355 Author chain B； PDBConstruct 1–355； 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 3lre

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3lre
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3lre
Deposition date deposition_date2010-02-11
Structure title titleCrystal Structure Analysis of Human Kinesin-8 Motor Domain
Keywords keywords;Motor protein, nucleotide binding, microtubule binding, ATP-binding, Cell projection, Cytoskeleton, Glycoprotein, Microtubule, Nucleotide-binding, Nucleus, Phosphoprotein, Protein transport, Transport ;; MOTOR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.40 Å
Radius of gyration Rg (electron density) rg_electron29.69 Å
Forward intensity I(0) i074987000.00
Molecular weight molecular_weight66646.0 kDa
Excluded volume excluded_volume82991 ų
Envelope volume envelope_volume108790 ų
Hydration-shell volume shell_volume30889 ų
Envelope diameter envelope_diameter97.9 Å
Shell Rg shell_rg36.40 Å
Envelope Rg envelope_rg29.38 Å
Shape Rg shape_rg29.69 Å
Total Rg total_rg30.32 Å
Total atoms total_atoms4665
Residues n_residues588
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 dmax96.6 Å
Rg (real space) rg_real30.44 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real7.4990e+07
I(0) uncertainty (real space) i0_real_error9.6480e+05
Rg (reciprocal space) rg_reciprocal30.43 Å
I(0) (reciprocal space) i0_reciprocal74990000.0000
Solution quality estimate total_estimate0.8902
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.9 Å
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.713
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha21170000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.913
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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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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3lrea_
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.37.1.0 — automated matches
Domain ID domain_idd3lreb_
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.37.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3lreA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology850 — Kinesin
Homologous superfamily homologous superfamily10 — Kinesin motor domain
Domain ID domain_id3lreB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology850 — Kinesin
Homologous superfamily homologous superfamily10 — Kinesin motor domain
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8. Citations (1)

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9. Files and Curves (10)