SAXSdb — 1s35

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

Spectrin beta chain, erythrocyte

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1063–1275	Fragment：repeats 8 and 9 Mutation：L1063E	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M Sodium Citrate, 0.3 M Ammonium Sulfate, 1.2-1.3 M Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.259

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 1S35	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EDU Crystal structure of the ankyrin-binding domain of human erythroid spectrin Deposited 2008-09-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1692–1907（216 aa） Fragment：Spectrin 14-Spectrin 15 di-repeat	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；0.1M bis-tris-propane, pH 6.2, 0.2M KSCN, 20% PEG 3,350, 3-10mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.10 Å R-free 0.252
3F57 Crystal structure of human erythroid beta spectrin repeats 14 and 15 (ankyrin binding domain) Deposited 2008-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1686–1907（222 aa） Fragment：HUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN BINDING DOMAIN): UNP RESIDUES 1686-1907	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；30% PEG 3350, 0.2 M NaCl, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.322
3F57 Crystal structure of human erythroid beta spectrin repeats 14 and 15 (ankyrin binding domain) Deposited 2008-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1686–1907（222 aa） Fragment：HUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN BINDING DOMAIN): UNP RESIDUES 1686-1907	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；30% PEG 3350, 0.2 M NaCl, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.322
3KBT Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK) Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.292
3KBT Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK) Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.292
3KBU Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Mutation：E1680C	HG MERCURY (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.277
3KBU Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Mutation：E1680C	HG MERCURY (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.277
3LBX Crystal Structure of the Erythrocyte Spectrin Tetramerization Domain Complex Deposited 2010-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1902–2084（183 aa） Fragment：UNP residues 1902-2084	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES pH 6.5, 10% PEG-6000, 10% glycerol, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.299

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPTB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–214； UniProt 1063–1275

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	1s35
Deposition date deposition_date	2004-01-12
Structure title title	Crystal Structure of Repeats 8 and 9 of Human Erythroid Spectrin
Keywords keywords	two repeats of spectrin, alpha helical linker region, 3-helix coiled-coils, beta spectrin, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	29.31 Å
Radius of gyration Rg (electron density) rg_electron	30.24 Å
Forward intensity I(0) i0	11112700.00
Molecular weight molecular_weight	24024.0 kDa
Excluded volume excluded_volume	29463 Å³
Envelope volume envelope_volume	40203 Å³
Hydration-shell volume shell_volume	13892 Å³
Envelope diameter envelope_diameter	113.1 Å
Shell Rg shell_rg	29.73 Å
Envelope Rg envelope_rg	31.52 Å
Shape Rg shape_rg	30.27 Å
Total Rg total_rg	30.09 Å
Total atoms total_atoms	1689
Residues n_residues	211
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	113.1 Å
Rg (real space) rg_real	30.04 Å
Rg uncertainty (real space) rg_real_error	1.80 Å
I(0) (real space) i0_real	1.1110e+07
I(0) uncertainty (real space) i0_real_error	2.2610e+05
Rg (reciprocal space) rg_reciprocal	29.73 Å
I(0) (reciprocal space) i0_reciprocal	11110000.0000
Solution quality estimate total_estimate	0.6332
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.8 Å
Skewness Skewness skewness	0.711
Kurtosis Kurtosis kurtosis	-0.248
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	862400.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.106; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.019; Smooth: 0.892

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Spectrin beta chain, erythrocyte
Molecular weight formula_weight	24269.8 kDa
Mutation mutation	L1063E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1871

MEQAFLQDLDDFQAWLSITQKAVASEDMPESLPEAEQLLQQHAGIKDEIDGHQDSYQRVKESGEKVIQGQTDPEYLLLGQRLEGLDTGWDALGRMWESRSHTLAQCLGFQEFQKDAKQAEAILSNQEYTLAHLEPPDSLEAAEAGIRKFEDFLGSMENNRDKVLSPVDSGNKLVAEGNLYSDKIKEKVQLIEDRHRKNNEKAQEASVLLRDNLE

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1s35a1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.1 — Spectrin repeat
Family Family family	a.7.1.1 — Spectrin repeat

Domain ID domain_id	d1s35a2
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.1 — Spectrin repeat
Family Family family	a.7.1.1 — Spectrin repeat

CATH v4.4 (2 domains)

Domain ID domain_id	1s35A01
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	60 —

Domain ID domain_id	1s35A02
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	60 —

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8. Citations (1)

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Unit-cell length a length_a	122.151 Å
Unit-cell length b length_b	122.151 Å
Unit-cell length c length_c	49.548 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	45.920 Å
R factor r_factor	—
R_work r_work	0.2220
R_free r_free	0.2590

fit	/app/data/saxs_computation/s3/1s35/1s35.fit
pddf	/app/data/pr_computation/s3/1s35/1s35.pr.out
profile	/app/data/saxs_computation/s3/1s35/1s35.dat

Crystal Structure of Repeats 8 and 9 of Human Erythroid Spectrin

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

Spectrin beta chain, erythrocyte

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