SAXSdb — 3eab

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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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 112–196	Fragment：UNP residues 112 to 196	CHMP1b × 1 （B2RA72）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 112–196	Fragment：UNP residues 112 to 196	CHMP1b × 1 （B2RA72）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 112–196	Fragment：UNP residues 112 to 196	CHMP1b × 1 （B2RA72）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 112–196	Fragment：UNP residues 112 to 196	CHMP1b × 1 （B2RA72）	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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 112–196	Fragment：UNP residues 112 to 196	CHMP1b × 1 （B2RA72）	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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 112–196	Fragment：UNP residues 112 to 196	CHMP1b × 1 （B2RA72）	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

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 3EAB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3VFD Human spastin AAA domain Deposited 2012-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
6PEN Structure of Spastin Hexamer (whole model) in complex with substrate peptide Deposited 2019-06-20	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 × 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 ligand/ion 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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPAST_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–89； UniProt 112–196 Author chain B； PDBConstruct 5–89； UniProt 112–196 Author chain C； PDBConstruct 5–89； UniProt 112–196 Author chain D； PDBConstruct 5–89； UniProt 112–196 Author chain E； PDBConstruct 5–89； UniProt 112–196 Author chain F； PDBConstruct 5–89； UniProt 112–196

CHMP1b

Homo sapiens

UniProt B2RA72

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 145–194	Fragment：UNP residues 145 to 194	Spastin × 1 （Q9UBP0）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 145–194	Fragment：UNP residues 145 to 194	Spastin × 1 （Q9UBP0）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 145–194	Fragment：UNP residues 145 to 194	Spastin × 1 （Q9UBP0）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain J； UniProt 145–194	Fragment：UNP residues 145 to 194	Spastin × 1 （Q9UBP0）	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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain K； UniProt 145–194	Fragment：UNP residues 145 to 194	Spastin × 1 （Q9UBP0）	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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 145–194	Fragment：UNP residues 145 to 194	Spastin × 1 （Q9UBP0）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	B2RA72_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–50； UniProt 145–194 Author chain H； PDBConstruct 1–50； UniProt 145–194 Author chain I； PDBConstruct 1–50； UniProt 145–194 Author chain J； PDBConstruct 1–50； UniProt 145–194 Author chain K； PDBConstruct 1–50； UniProt 145–194 Author chain L； PDBConstruct 1–50； UniProt 145–194

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	3eab
Deposition date deposition_date	2008-08-25
Structure title title	Crystal structure of Spastin MIT in complex with ESCRT III
Keywords keywords	;Spastin, CHMP, MIT, ESCRT, Alternative splicing, ATP-binding, Cytoplasm, Disease mutation, Hereditary spastic paraplegia, Nucleotide-binding, Nucleus, Polymorphism, CELL CYCLE ;; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	44.77 Å
Radius of gyration Rg (electron density) rg_electron	45.21 Å
Forward intensity I(0) i0	123031000.00
Molecular weight molecular_weight	85670.0 kDa
Excluded volume excluded_volume	105970 Å³
Envelope volume envelope_volume	173480 Å³
Hydration-shell volume shell_volume	37437 Å³
Envelope diameter envelope_diameter	156.6 Å
Shell Rg shell_rg	40.83 Å
Envelope Rg envelope_rg	44.73 Å
Shape Rg shape_rg	45.17 Å
Total Rg total_rg	45.06 Å
Total atoms total_atoms	5977
Residues n_residues	759
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	157.4 Å
Rg (real space) rg_real	45.12 Å
Rg uncertainty (real space) rg_real_error	2.62 Å
I(0) (real space) i0_real	1.2300e+08
I(0) uncertainty (real space) i0_real_error	2.8040e+06
Rg (reciprocal space) rg_reciprocal	44.78 Å
I(0) (reciprocal space) i0_reciprocal	123000000.0000
Solution quality estimate total_estimate	0.8126
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	54.0 Å
Skewness Skewness skewness	0.344
Kurtosis Kurtosis kurtosis	-0.561
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3186000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.718; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.617; Smooth: 0.791

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Spastin
Molecular weight formula_weight	10314.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5977

MGSMEAERVRVFHKQAFEYISIALRIDEDEKAGQKEQAVEWYKKGIEELEKGIAVIVTGQGEQCERARRLQAKMMTNLVMAKDRLQLLE

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CHMP1b
Molecular weight formula_weight	5420.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

QVDMLLQEMADEAGLDLNMELPQGQTGSVGTSVASAEQDELSQRLARLRD

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	Escherichia coli

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3eabA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	3eabB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	3eabC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	3eabD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	3eabE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	3eabF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	3eabG00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	3eabI00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	440 —

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8. Citations (1)

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Unit-cell length a length_a	151.967 Å
Unit-cell length b length_b	95.493 Å
Unit-cell length c length_c	100.360 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	47.650 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2680

fit	/app/data/saxs_computation/ea/3eab/3eab.fit
pddf	/app/data/pr_computation/ea/3eab/3eab.pr.out
profile	/app/data/saxs_computation/ea/3eab/3eab.dat

Crystal structure of Spastin MIT in complex with ESCRT III

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

CHMP1b

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)