7ytd

Cryo-EM structure of four human FcmR bound to IgM-Fc/J

Method: ELECTRON MICROSCOPY Dmax: 176.7 Å Quality: GOOD

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

Immunoglobulin heavy constant mu

Homo sapiens

UniProt P01871

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 heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain A; UniProt 222–452 Chain B; UniProt 222–452 Chain C; UniProt 222–452 Chain D; UniProt 222–452 Chain E; UniProt 222–452 Chain F; UniProt 222–452 Chain G; UniProt 222–452 Chain H; UniProt 222–452 Chain K; UniProt 222–452 Chain L; UniProt 222–452 Not recorded Immunoglobulin J chain × 1 (P01591) Fas apoptotic inhibitory molecule 3 × 4 (O60667) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.71 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.

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGHM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–231; UniProt 222–452 Author chain B; PDBConstruct 1–231; UniProt 222–452 Author chain C; PDBConstruct 1–231; UniProt 222–452 Author chain D; PDBConstruct 1–231; UniProt 222–452 Author chain E; PDBConstruct 1–231; UniProt 222–452 Author chain F; PDBConstruct 1–231; UniProt 222–452 Author chain G; PDBConstruct 1–231; UniProt 222–452 Author chain H; PDBConstruct 1–231; UniProt 222–452 Author chain K; PDBConstruct 1–231; UniProt 222–452 Author chain L; PDBConstruct 1–231; UniProt 222–452

Immunoglobulin J chain

Homo sapiens

UniProt P01591

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 heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain J; UniProt 24–159 Not recorded Immunoglobulin heavy constant mu × 10 (P01871) Fas apoptotic inhibitory molecule 3 × 4 (O60667) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.71 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.

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGJ_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain J; PDBConstruct 1–136; UniProt 24–159

Fas apoptotic inhibitory molecule 3

Homo sapiens

UniProt O60667

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 heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain R; UniProt 18–124 Chain S; UniProt 18–124 Chain U; UniProt 18–124 Chain V; UniProt 18–124 Not recorded Immunoglobulin heavy constant mu × 10 (P01871) Immunoglobulin J chain × 1 (P01591) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.71 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.

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

View Construct and Data Evidence
UniProt name FAIM3_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain R; PDBConstruct 1–107; UniProt 18–124 Author chain S; PDBConstruct 1–107; UniProt 18–124 Author chain U; PDBConstruct 1–107; UniProt 18–124 Author chain V; PDBConstruct 1–107; UniProt 18–124

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 7ytd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ytd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ytd
Deposition date deposition_date2022-08-14
Structure title titleCryo-EM structure of four human FcmR bound to IgM-Fc/J
Keywords keywordsimmunoglobin M, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier55.29
Radius of gyration Rg (electron density) rg_electron55.27
Forward intensity I(0) i01396580000.00
Molecular weight molecular_weight308810.0 kDa
Excluded volume excluded_volume385480 ų
Envelope volume envelope_volume613000 ų
Hydration-shell volume shell_volume93792 ų
Envelope diameter envelope_diameter189.0
Shell Rg shell_rg55.92
Envelope Rg envelope_rg54.88
Shape Rg shape_rg55.31
Total Rg total_rg55.15
Total atoms total_atoms21693
Residues n_residues2777
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 dmax176.7
Rg (real space) rg_real55.38
Rg uncertainty (real space) rg_real_error1.54
I(0) (real space) i0_real1.3970e+09
I(0) uncertainty (real space) i0_real_error2.6880e+07
Rg (reciprocal space) rg_reciprocal55.20
I(0) (reciprocal space) i0_reciprocal1396000000.0000
Solution quality estimate total_estimate0.8432
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.8
Skewness Skewness skewness0.391
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha135100000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.210

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id7ytdA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdR01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdS01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdU01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ytdV01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)