SAXSdb — 6pek

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

Spastin

Homo sapiens

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 × 6 PDB declaration: hexameric（6） 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	Not recorded	substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU × 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 6PEK	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
6PEN Structure of Spastin Hexamer (whole model) in complex with substrate peptide Deposited 2019-06-20	Different construct Different mutation/modification Different oligomeric state	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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） Chain F 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6pek
Deposition date deposition_date	2019-06-20
Structure title title	Structure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide
Keywords keywords	AAA+ ATPase, Microtubule Severing, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	38.63 Å
Radius of gyration Rg (electron density) rg_electron	38.35 Å
Forward intensity I(0) i0	381803000.00
Molecular weight molecular_weight	158300.0 kDa
Excluded volume excluded_volume	198200 Å³
Envelope volume envelope_volume	264790 Å³
Hydration-shell volume shell_volume	56711 Å³
Envelope diameter envelope_diameter	128.4 Å
Shell Rg shell_rg	44.87 Å
Envelope Rg envelope_rg	38.36 Å
Shape Rg shape_rg	38.29 Å
Total Rg total_rg	38.90 Å
Total atoms total_atoms	11106
Residues n_residues	1405
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	125.5 Å
Rg (real space) rg_real	38.62 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	3.8180e+08
I(0) uncertainty (real space) i0_real_error	7.0060e+06
Rg (reciprocal space) rg_reciprocal	38.63 Å
I(0) (reciprocal space) i0_reciprocal	381800000.0000
Solution quality estimate total_estimate	0.8905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.8 Å
Skewness Skewness skewness	0.295
Kurtosis Kurtosis kurtosis	-0.544
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	173100000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.844

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Spastin
Molecular weight formula_weight	54498.3 kDa
EC 编号 ec_number	5.6.1.1
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	11106

MAAKRSSGAAPAPASASAPAPVPGGEAERVRVFHKQAFEYISIALRIDEDEKAGQKEQAVEWYKKGIEELEKGIAVIVTGQGEQCERARRLQAKMMTNLVMAKDRLQLLESGAVPKRKDPLTHTSNSLPRSKTVMKTGSAGLSGHHRAPSYSGLSMVSGVKQGSGPAPTTHKGTPKTNRTNKPSTPTTATRKKKDLKNFRNVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDEVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFGDTTV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU
Molecular weight formula_weight	1479.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

EYEYEYEYEY

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	119984

fit	/app/data/saxs_computation/pe/6pek/6pek.fit
pddf	/app/data/pr_computation/pe/6pek/6pek.pr.out
profile	/app/data/saxs_computation/pe/6pek/6pek.dat

Structure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide

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

Spastin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)