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8bpe

8:1 binding of FcMR on IgM pentameric core

Method: ELECTRON MICROSCOPY Dmax: 175.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 Other combination Heteromer Protein × 19 其他Polymer 3 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain I； UniProt 18–251 Chain M； UniProt 18–251 Chain N； UniProt 18–251 Chain O； UniProt 18–251 Chain P； UniProt 18–251 Chain Q； UniProt 18–251 Chain R； UniProt 18–251 Chain S； UniProt 18–251 Not recorded Immunoglobulin heavy constant mu × 10 Immunoglobulin J chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.63 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.

Other PDB Difference from Current Entry 8BPE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7YSG Cryo-EM structure of human FcmR bound to sIgM Deposited 2022-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain R 18–124（107 aa）
Chain S 18–124（107 aa）
Chain U 18–124（107 aa）
Chain V 18–124（107 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
7YTC Cryo-EM structure of human FcmR bound to IgM-Fc/J Deposited 2022-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 18–124（107 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
7YTD Cryo-EM structure of four human FcmR bound to IgM-Fc/J Deposited 2022-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain R 18–124（107 aa）
Chain S 18–124（107 aa）
Chain U 18–124（107 aa）
Chain V 18–124（107 aa）
Not recorded 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
7YTE crystal structure of human FcmR-D1 bound to IgM C4-domain Deposited 2022-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 18–124（107 aa）
Chain D 18–124（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1:1 ratio of protein:reservoir solution containing 0.1 M Ammonium citrate tribasic (pH 7.0) and 12% (w/v) PEG 3,350
Resolution 3.00 Å R-free 0.269
8BPF FcMR binding at subunit Fcu1 of IgM pentamer Deposited 2022-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 18–251（234 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BPG FcMR binding at subunit Fcu3 of IgM pentamer Deposited 2022-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 18–251（234 aa）
Chain B 18–251（234 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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 2
Chains and sequence ranges Author chain I； PDBConstruct 1–234； UniProt 18–251 Author chain M； PDBConstruct 1–234； UniProt 18–251 Author chain N； PDBConstruct 1–234； UniProt 18–251 Author chain O； PDBConstruct 1–234； UniProt 18–251 Author chain P； PDBConstruct 1–234； UniProt 18–251 Author chain Q； PDBConstruct 1–234； UniProt 18–251 Author chain R； PDBConstruct 1–234； UniProt 18–251 Author chain S； PDBConstruct 1–234； UniProt 18–251

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 8bpe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8bpe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8bpe
Deposition date deposition_date2022-11-16
Structure title title8:1 binding of FcMR on IgM pentameric core
Keywords keywordsIgM Fc receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier53.60 Å
Radius of gyration Rg (electron density) rg_electron53.46 Å
Forward intensity I(0) i01746360000.00
Molecular weight molecular_weight344800.0 kDa
Excluded volume excluded_volume430280 ų
Envelope volume envelope_volume705950 ų
Hydration-shell volume shell_volume108820 ų
Envelope diameter envelope_diameter190.5 Å
Shell Rg shell_rg57.54 Å
Envelope Rg envelope_rg52.88 Å
Shape Rg shape_rg53.51 Å
Total Rg total_rg53.43 Å
Total atoms total_atoms24195
Residues n_residues3104
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 dmax175.5 Å
Rg (real space) rg_real53.59 Å
Rg uncertainty (real space) rg_real_error1.48 Å
I(0) (real space) i0_real1.7460e+09
I(0) uncertainty (real space) i0_real_error3.1340e+07
Rg (reciprocal space) rg_reciprocal53.60 Å
I(0) (reciprocal space) i0_reciprocal1746000000.0000
Solution quality estimate total_estimate0.8529
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.5 Å
Skewness Skewness skewness0.403
Kurtosis Kurtosis kurtosis-0.125
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha203100000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.592
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id8bpeA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8bpeK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)