5oba

Structure of a modified mouse H-chain ferritin with a lanthanide binding motif

Method: X-RAY DIFFRACTION Dmax: 135.4 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 1–177 Chain B; UniProt 1–177 Chain C; UniProt 1–177 Chain D; UniProt 1–177 Chain E; UniProt 1–177 Chain F; UniProt 1–177 Chain G; UniProt 1–177 Chain H; UniProt 1–177 Chain I; UniProt 1–177 Chain J; UniProt 1–177 Chain K; UniProt 1–177 Chain L; UniProt 1–177 Chain M; UniProt 1–177 Chain N; UniProt 1–177 Chain O; UniProt 1–177 Chain P; UniProt 1–177 Chain Q; UniProt 1–177 Chain R; UniProt 1–177 Chain S; UniProt 1–177 Chain T; UniProt 1–177 Chain U; UniProt 1–177 Chain V; UniProt 1–177 Chain W; UniProt 1–177 Chain X; UniProt 1–177 Mutation:H177G FE FE (III) ION × 32 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;294 K;Ammonium sulphate, Tris-HCl Resolution 2.85 Å R-free 0.170

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 1–177; UniProt 1–177 Author chain B; PDBConstruct 1–177; UniProt 1–177 Author chain C; PDBConstruct 1–177; UniProt 1–177 Author chain D; PDBConstruct 1–177; UniProt 1–177 Author chain E; PDBConstruct 1–177; UniProt 1–177 Author chain F; PDBConstruct 1–177; UniProt 1–177 Author chain G; PDBConstruct 1–177; UniProt 1–177 Author chain H; PDBConstruct 1–177; UniProt 1–177 Author chain I; PDBConstruct 1–177; UniProt 1–177 Author chain J; PDBConstruct 1–177; UniProt 1–177 Author chain K; PDBConstruct 1–177; UniProt 1–177 Author chain L; PDBConstruct 1–177; UniProt 1–177 Author chain M; PDBConstruct 1–177; UniProt 1–177 Author chain N; PDBConstruct 1–177; UniProt 1–177 Author chain O; PDBConstruct 1–177; UniProt 1–177 Author chain P; PDBConstruct 1–177; UniProt 1–177 Author chain Q; PDBConstruct 1–177; UniProt 1–177 Author chain R; PDBConstruct 1–177; UniProt 1–177 Author chain S; PDBConstruct 1–177; UniProt 1–177 Author chain T; PDBConstruct 1–177; UniProt 1–177 Author chain U; PDBConstruct 1–177; UniProt 1–177 Author chain V; PDBConstruct 1–177; UniProt 1–177 Author chain W; PDBConstruct 1–177; UniProt 1–177 Author chain X; PDBConstruct 1–177; UniProt 1–177

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 5oba

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5oba
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5oba
Deposition date deposition_date2017-06-26
Structure title titleStructure of a modified mouse H-chain ferritin with a lanthanide binding motif
Keywords keywordsferritin, lanthanide, metal transport; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.91
Radius of gyration Rg (electron density) rg_electron52.91
Forward intensity I(0) i03581290000.00
Molecular weight molecular_weight484520.0 kDa
Excluded volume excluded_volume598500 ų
Envelope volume envelope_volume967050 ų
Hydration-shell volume shell_volume148480 ų
Envelope diameter envelope_diameter137.3
Shell Rg shell_rg63.75
Envelope Rg envelope_rg47.88
Shape Rg shape_rg52.90
Total Rg total_rg53.24
Total atoms total_atoms33994
Residues n_residues4155
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 dmax135.4
Rg (real space) rg_real53.37
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real3.5810e+09
I(0) uncertainty (real space) i0_real_error5.5360e+07
Rg (reciprocal space) rg_reciprocal54.35
I(0) (reciprocal space) i0_reciprocal3586000000.0000
Solution quality estimate total_estimate0.8004
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary88.7
Skewness Skewness skewness-0.384
Kurtosis Kurtosis kurtosis-0.638
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha146600000000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 55 domains

SCOP 2.08 (31 domains)

Domain ID domain_idd5obaa_
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_idd5obab_
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_idd5obac_
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_idd5obad_
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_idd5obae_
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_idd5obaf1
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_idd5obaf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5obag1
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_idd5obag2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5obah_
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_idd5obai_
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_idd5obaj_
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_idd5obak_
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_idd5obal1
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_idd5obal2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5obam_
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_idd5oban_
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_idd5obao_
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_idd5obap_
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_idd5obaq_
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_idd5obar1
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_idd5obar2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5obas1
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_idd5obas2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5obat_
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_idd5obau_
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_idd5obav1
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_idd5obav2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5obaw_
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_idd5obax1
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_idd5obax2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (24 domains)

Domain ID domain_id5obaA00
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_id5obaB00
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_id5obaC00
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_id5obaD00
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_id5obaE00
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_id5obaF00
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_id5obaG00
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_id5obaH00
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_id5obaI00
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_id5obaJ00
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_id5obaK00
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_id5obaL00
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_id5obaM00
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_id5obaN00
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_id5obaO00
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_id5obaP00
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_id5obaQ00
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_id5obaR00
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_id5obaS00
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_id5obaT00
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_id5obaU00
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_id5obaV00
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_id5obaW00
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_id5obaX00
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)