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3edv

Crystal Structure of Repeats 14-16 of Beta2-Spectrin

Method: X-RAY DIFFRACTION Dmax: 135.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spectrin beta chain, brain 1

Homo sapiens

UniProt Q01082

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1697–2015 Chain B； UniProt 1697–2015 Fragment：Spectrin repeats 14-16 MG MAGNESIUM ION × 13 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.95 Å R-free 0.250
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1697–2015 Fragment：Spectrin repeats 14-16 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.95 Å R-free 0.250
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1697–2015 Fragment：Spectrin repeats 14-16 MG MAGNESIUM ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.95 Å R-free 0.250

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 3EDV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AA2 CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN Deposited 1997-01-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 173–280（108 aa） Fragment：F-ACTIN BINDING DOMAIN RESIDUES 173 - 281
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.6；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 8000, 100 MM SODIUM CACODYLATE, PH 6.6
Resolution 2.00 Å R-free 0.210
1BKR CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANGSTROM RESOLUTION Deposited 1998-07-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 172–280（109 aa） Fragment：F-ACTIN BINDING DOMAIN RESIDUES 173 - 281
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.6；PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE PH 6.6 PEG8K 30% (W/V)
Resolution 1.10 Å R-free 0.187

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPTB2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–323； UniProt 1697–2015 Author chain B； PDBConstruct 5–323； UniProt 1697–2015

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 3edv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3edv
Deposition date deposition_date2008-09-03
Structure title titleCrystal Structure of Repeats 14-16 of Beta2-Spectrin
Keywords keywords;spectrin repeat, coiled coil, Actin capping, Actin-binding, Alternative splicing, Calmodulin-binding, Cytoplasm, Cytoskeleton, Glycoprotein, Membrane, Phosphoprotein, Polymorphism, STRUCTURAL PROTEIN ;; STRUCTURAL 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_guinier51.63 Å
Radius of gyration Rg (electron density) rg_electron53.85 Å
Forward intensity I(0) i095697500.00
Molecular weight molecular_weight75862.0 kDa
Excluded volume excluded_volume93504 ų
Envelope volume envelope_volume149790 ų
Hydration-shell volume shell_volume29508 ų
Envelope diameter envelope_diameter211.1 Å
Shell Rg shell_rg41.33 Å
Envelope Rg envelope_rg55.03 Å
Shape Rg shape_rg53.76 Å
Total Rg total_rg53.51 Å
Total atoms total_atoms5333
Residues n_residues643
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 dmax135.5 Å
Rg (real space) rg_real46.10 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real9.0650e+07
I(0) uncertainty (real space) i0_real_error1.5200e+06
Rg (reciprocal space) rg_reciprocal50.67 Å
I(0) (reciprocal space) i0_reciprocal95420000.0000
Solution quality estimate total_estimate0.6438
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.1 Å
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.755
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.6514
Highest regularization parameter α highest_alpha2804000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.012; Oscil: 0.917; Stabil: 0.981; Sysdev: 0.000; Positv: 1.000; Valcen: 0.681; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3edvA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3edvA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3edvB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3edvB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily60 —
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8. Citations (1)

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9. Files and Curves (10)