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6pen

Structure of Spastin Hexamer (whole model) in complex with substrate peptide

Method: ELECTRON MICROSCOPY Dmax: 122.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spastin

Homo sapiens

UniProt Q9UBP0

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain A； UniProt 87–584 Chain B； UniProt 87–584 Chain C； UniProt 87–584 Chain D； UniProt 87–584 Chain E； UniProt 87–584 Chain F； UniProt 87–584 Not recorded EYEYEYEYEY × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 5 BEF BERYLLIUM TRIFLUORIDE ION × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.20 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 6PEN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 112–196（85 aa） Fragment：UNP residues 112 to 196
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 112–196（85 aa） Fragment：UNP residues 112 to 196
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 112–196（85 aa） Fragment：UNP residues 112 to 196
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 112–196（85 aa） Fragment：UNP residues 112 to 196
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 112–196（85 aa） Fragment：UNP residues 112 to 196
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 112–196（85 aa） Fragment：UNP residues 112 to 196
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.50 Å R-free 0.268
3VFD Human spastin AAA domain Deposited 2012-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–616（389 aa） Fragment：AAA domain
Mutation：E442Q SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；1.6M (NH3)2SO4, 0.1M MES monohydrate (pH 6.5),10% 1,4-dioxane and 4% benzamidine HCl, 1mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 3.30 Å R-free 0.275
5Z6Q Crystal structure of AAA of Spastin Deposited 2018-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–616（388 aa） Fragment：UNP residues 229-616
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3M (NH4)2SO4, 100mM NH4Cl
Resolution 3.00 Å R-free 0.276
5Z6R SPASTIN AAA WITH ATP Deposited 2018-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–616（388 aa） Fragment：UNP RESIDUES 229-616
Mutation：E442Q ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；25MM TRIS-HCL, 1MM DTT, 1MM MGCL2, 1MM ATP, 2% PEG 3350, 20MM KSCN
Resolution 3.00 Å R-free 0.279
6PEK Structure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide Deposited 2019-06-20 Different construct Different mutation/modification Different oligomeric state Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 87–584（498 aa）
Chain B 87–584（498 aa）
Chain C 87–584（498 aa）
Chain D 87–584（498 aa）
Chain E 87–584（498 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 BEF BERYLLIUM TRIFLUORIDE ION × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7S7J Structure of Human SPASTIN-IST1 complex. Deposited 2021-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 112–195（84 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 CA CALCIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；40% v/v PEG 300, 100 mM Sodium cacodylate / Hydrochloric acid pH=6.5, 200 mM Calcium Acetate
Resolution 1.15 Å R-free 0.157

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPAST_HUMAN
Isoform Q9UBP0-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–498； UniProt 87–584 Author chain B； PDBConstruct 1–498； UniProt 87–584 Author chain C； PDBConstruct 1–498； UniProt 87–584 Author chain D； PDBConstruct 1–498； UniProt 87–584 Author chain E； PDBConstruct 1–498； UniProt 87–584 Author chain F； PDBConstruct 1–498； UniProt 87–584

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 6pen

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6pen
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6pen
Deposition date deposition_date2019-06-20
Structure title titleStructure of Spastin Hexamer (whole model) in complex with substrate peptide
Keywords keywordsAAA+ ATPase, Microtubule Severing, 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_guinier40.36 Å
Radius of gyration Rg (electron density) rg_electron39.78 Å
Forward intensity I(0) i0516194000.00
Molecular weight molecular_weight180270.0 kDa
Excluded volume excluded_volume223560 ų
Envelope volume envelope_volume319130 ų
Hydration-shell volume shell_volume64550 ų
Envelope diameter envelope_diameter128.4 Å
Shell Rg shell_rg47.21 Å
Envelope Rg envelope_rg39.58 Å
Shape Rg shape_rg39.76 Å
Total Rg total_rg40.24 Å
Total atoms total_atoms12675
Residues n_residues1722
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 dmax122.0 Å
Rg (real space) rg_real40.27 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real5.1620e+08
I(0) uncertainty (real space) i0_real_error7.5430e+06
Rg (reciprocal space) rg_reciprocal40.36 Å
I(0) (reciprocal space) i0_reciprocal516200000.0000
Solution quality estimate total_estimate0.8745
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.8 Å
Skewness Skewness skewness0.210
Kurtosis Kurtosis kurtosis-0.597
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha190700000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.433
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)