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3f31

Crystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain

Method: X-RAY DIFFRACTION Dmax: 105.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spectrin alpha chain, brain

Homo sapiens

UniProt Q13813

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 1–147 Chain B； UniProt 1–147 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.30 Å R-free 0.280
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–147 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.30 Å R-free 0.280
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–147 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.30 Å R-free 0.280

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 3F31 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2FOT Crystal structure of the complex between calmodulin and alphaII-spectrin Deposited 2006-01-13 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 C 1172–1211（40 aa） Fragment：Calmodulin binding domain
Mutation：L1211R CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；50mM Tris,pH 8.00, 30% PEG 8000, 0.1M ammonium-sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.45 Å R-free 0.269
3FB2 Crystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a. Deposited 2008-11-18 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1337–1544（208 aa） Fragment：Repeats 15 and 16
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch crystallization under oil；pH 5；277 K；12% PEG 20000, 0.1M magnesium sulfate, 0.1M sodium acetate, pH 5.0, microbatch crystallization under oil, temperature 277K
Resolution 2.30 Å R-free 0.248
3FB2 Crystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a. Deposited 2008-11-18 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1337–1544（208 aa） Fragment：Repeats 15 and 16
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch crystallization under oil；pH 5；277 K；12% PEG 20000, 0.1M magnesium sulfate, 0.1M sodium acetate, pH 5.0, microbatch crystallization under oil, temperature 277K
Resolution 2.30 Å R-free 0.248
5FW9 Human Spectrin SH3 domain D48G, E7Y, K60Y Deposited 2016-02-12 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 965–1025（61 aa） Fragment：SH3 DOMAIN, RESIDUES 965-1025
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å R-free 0.249
5FWB Human Spectrin SH3 domain D48G, E7F, K60F Deposited 2016-02-12 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 965–1022（58 aa） Fragment：SH3, UNP RESIDUES 965-1025
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.236
5FWC Human Spectrin SH3 domain D48G, E7A, K60A Deposited 2016-02-12 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 965–1022（58 aa） Fragment：SH3, RESIDUES 965-1022
Mutation：YES EDO 1,2-ETHANEDIOL × 2 NH4 AMMONIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.40 Å R-free 0.238
6ZEH Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580) Deposited 2020-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1025–1039（15 aa）
Mutation：N-terminal Vector derived sequence GHMGS MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5
Resolution 1.30 Å R-free 0.169
6ZEH Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580) Deposited 2020-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1025–1039（15 aa）
Mutation：N-terminal Vector derived sequence GHMGS MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5
Resolution 1.30 Å R-free 0.169

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

View Construct and Data Evidence
UniProt name SPTA2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–149； UniProt 1–147 Author chain B； PDBConstruct 3–149； UniProt 1–147

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 3f31

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3f31
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3f31
Deposition date deposition_date2008-10-30
Structure title titleCrystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain
Keywords keywords;lone helix followed by a triple helical bundle, Actin capping, Actin-binding, Alternative splicing, Calcium, Calmodulin-binding, Cytoplasm, Cytoskeleton, Phosphoprotein, Polymorphism, SH3 domain, SPECTRIN, ACTIN BINDING, STRUCTURAL PROTEIN ;; ACTIN BINDING, 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_guinier26.55 Å
Radius of gyration Rg (electron density) rg_electron26.37 Å
Forward intensity I(0) i019661200.00
Molecular weight molecular_weight32943.0 kDa
Excluded volume excluded_volume41000 ų
Envelope volume envelope_volume57014 ų
Hydration-shell volume shell_volume20115 ų
Envelope diameter envelope_diameter112.1 Å
Shell Rg shell_rg30.49 Å
Envelope Rg envelope_rg27.41 Å
Shape Rg shape_rg26.33 Å
Total Rg total_rg26.98 Å
Total atoms total_atoms2322
Residues n_residues277
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 dmax105.3 Å
Rg (real space) rg_real26.96 Å
Rg uncertainty (real space) rg_real_error1.43 Å
I(0) (real space) i0_real1.9660e+07
I(0) uncertainty (real space) i0_real_error3.1660e+05
Rg (reciprocal space) rg_reciprocal26.84 Å
I(0) (reciprocal space) i0_reciprocal19660000.0000
Solution quality estimate total_estimate0.6654
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.3 Å
Skewness Skewness skewness0.713
Kurtosis Kurtosis kurtosis0.179
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2552000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.458; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.277; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3f31a_
Class classa — All alpha proteins
Fold Fold folda.7 — Spectrin repeat-like
Superfamily Superfamily superfamilya.7.1 — Spectrin repeat
Family Family familya.7.1.0 — automated matches
Domain ID domain_idd3f31b_
Class classa — All alpha proteins
Fold Fold folda.7 — Spectrin repeat-like
Superfamily Superfamily superfamilya.7.1 — Spectrin repeat
Family Family familya.7.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3f31A00
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_id3f31B00
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)