6s61

Apoferritin from mouse at 1.84 angstrom resolution

Method: ELECTRON MICROSCOPY Dmax: 139.8 Å Quality: GOOD

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

Ferritin heavy chain

Mus musculus

UniProt P09528

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 × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain A; UniProt 1–182 Chain B; UniProt 1–182 Chain C; UniProt 1–182 Chain D; UniProt 1–182 Chain E; UniProt 1–182 Chain F; UniProt 1–182 Chain G; UniProt 1–182 Chain H; UniProt 1–182 Chain I; UniProt 1–182 Chain J; UniProt 1–182 Chain K; UniProt 1–182 Chain L; UniProt 1–182 Chain M; UniProt 1–182 Chain N; UniProt 1–182 Chain O; UniProt 1–182 Chain P; UniProt 1–182 Chain Q; UniProt 1–182 Chain R; UniProt 1–182 Chain S; UniProt 1–182 Chain T; UniProt 1–182 Chain U; UniProt 1–182 Chain V; UniProt 1–182 Chain W; UniProt 1–182 Chain X; UniProt 1–182 Not recorded FE FE (III) ION × 6 ZN ZINC ION × 24 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.84 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.

26 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FRIH_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–182; UniProt 1–182 Author chain B; PDBConstruct 1–182; UniProt 1–182 Author chain C; PDBConstruct 1–182; UniProt 1–182 Author chain D; PDBConstruct 1–182; UniProt 1–182 Author chain E; PDBConstruct 1–182; UniProt 1–182 Author chain F; PDBConstruct 1–182; UniProt 1–182 Author chain G; PDBConstruct 1–182; UniProt 1–182 Author chain H; PDBConstruct 1–182; UniProt 1–182 Author chain I; PDBConstruct 1–182; UniProt 1–182 Author chain J; PDBConstruct 1–182; UniProt 1–182 Author chain K; PDBConstruct 1–182; UniProt 1–182 Author chain L; PDBConstruct 1–182; UniProt 1–182 Author chain M; PDBConstruct 1–182; UniProt 1–182 Author chain N; PDBConstruct 1–182; UniProt 1–182 Author chain O; PDBConstruct 1–182; UniProt 1–182 Author chain P; PDBConstruct 1–182; UniProt 1–182 Author chain Q; PDBConstruct 1–182; UniProt 1–182 Author chain R; PDBConstruct 1–182; UniProt 1–182 Author chain S; PDBConstruct 1–182; UniProt 1–182 Author chain T; PDBConstruct 1–182; UniProt 1–182 Author chain U; PDBConstruct 1–182; UniProt 1–182 Author chain V; PDBConstruct 1–182; UniProt 1–182 Author chain W; PDBConstruct 1–182; UniProt 1–182 Author chain X; PDBConstruct 1–182; UniProt 1–182

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 6s61

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6s61
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6s61
Deposition date deposition_date2019-07-02
Structure title titleApoferritin from mouse at 1.84 angstrom resolution
Keywords keywordsiron ion binding, ferroxidase, iron storage, cytoplasm, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier54.09
Radius of gyration Rg (electron density) rg_electron53.11
Forward intensity I(0) i03547750000.00
Molecular weight molecular_weight482520.0 kDa
Excluded volume excluded_volume596130 ų
Envelope volume envelope_volume967060 ų
Hydration-shell volume shell_volume148500 ų
Envelope diameter envelope_diameter137.5
Shell Rg shell_rg63.76
Envelope Rg envelope_rg47.86
Shape Rg shape_rg53.11
Total Rg total_rg53.41
Total atoms total_atoms66246
Residues n_residues4128
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax139.8
Rg (real space) rg_real53.55
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real3.5480e+09
I(0) uncertainty (real space) i0_real_error5.1850e+07
Rg (reciprocal space) rg_reciprocal54.54
I(0) (reciprocal space) i0_reciprocal3553000000.0000
Solution quality estimate total_estimate0.7919
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary86.8
Skewness Skewness skewness-0.392
Kurtosis Kurtosis kurtosis-0.638
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha328000000000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd6s61a_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61b_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61c_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61d_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61e_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61f_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61g_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61h_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61i_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61j_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61k_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61l_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61m_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61n_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61o_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61p_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61q_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61r_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61s_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61t_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61u_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61v_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61w_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin
Domain ID domain_idd6s61x_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin

CATH v4.4 (24 domains)

Domain ID domain_id6s61A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61C00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61D00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61E00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61F00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61G00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61H00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61I00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61J00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61K00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61L00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61M00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61N00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61O00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61P00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61Q00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61R00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61S00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61T00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61U00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61V00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61W00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle
Domain ID domain_id6s61X00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle

8. Citations (1)

9. Files and Curves (10)