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7yte

crystal structure of human FcmR-D1 bound to IgM C4-domain

Method: X-RAY DIFFRACTION Dmax: 95.5 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 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 18–124 Chain D； UniProt 18–124 Not recorded Ig mu chain C region secreted form × 2 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

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 7YTE 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 method 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 method 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 method 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
8BPE 8:1 binding of FcMR on IgM pentameric core Deposited 2022-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain I 18–251（234 aa）
Chain M 18–251（234 aa）
Chain N 18–251（234 aa）
Chain O 18–251（234 aa）
Chain P 18–251（234 aa）
Chain Q 18–251（234 aa）
Chain R 18–251（234 aa）
Chain S 18–251（234 aa）
Not recorded 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
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 experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 C； PDBConstruct 1–107； UniProt 18–124 Author chain D； 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 7yte

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7yte
Deposition date deposition_date2022-08-14
Structure title titlecrystal structure of human FcmR-D1 bound to IgM C4-domain
Keywords keywordsFcmR, immunoglobin M, IMMUNE SYSTEM; IMMUNE SYSTEM
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_guinier26.89 Å
Radius of gyration Rg (electron density) rg_electron26.64 Å
Forward intensity I(0) i039267200.00
Molecular weight molecular_weight47959.0 kDa
Excluded volume excluded_volume59849 ų
Envelope volume envelope_volume76460 ų
Hydration-shell volume shell_volume25620 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg32.06 Å
Envelope Rg envelope_rg27.07 Å
Shape Rg shape_rg26.61 Å
Total Rg total_rg27.34 Å
Total atoms total_atoms3363
Residues n_residues436
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 dmax95.5 Å
Rg (real space) rg_real27.14 Å
Rg uncertainty (real space) rg_real_error0.93 Å
I(0) (real space) i0_real3.9270e+07
I(0) uncertainty (real space) i0_real_error6.0630e+05
Rg (reciprocal space) rg_reciprocal27.06 Å
I(0) (reciprocal space) i0_reciprocal39270000.0000
Solution quality estimate total_estimate0.8264
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.597
Kurtosis Kurtosis kurtosis-0.060
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6888000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.686; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.706; Smooth: 0.975
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7yteC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7yteD01
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)