Cryo-EM structure of the human IgM-Fc hexamer

Method: ELECTRON MICROSCOPY D_max: 191.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uo3
deposition_date	2025-04-25
title	Cryo-EM structure of the human IgM-Fc hexamer
keywords	Complex, polymeric antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	59.10 Å
rg_electron	58.96 Å
i0	1173210000.00
molecular_weight	283780.0 kDa
excluded_volume	353680 Å³
envelope_volume	602120 Å³
shell_volume	83646 Å³
envelope_diameter	186.3 Å
shell_rg	61.50 Å
envelope_rg	57.90 Å
shape_rg	58.95 Å
total_rg	59.06 Å
total_atoms	19980
n_residues	2568
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	191.5 Å
rg_real	59.11 Å
rg_real_error	1.84 Å
i0_real	1.1730e+09
i0_real_error	2.5060e+07
rg_reciprocal	59.06 Å
i0_reciprocal	1173000000.0000
total_estimate	0.8473
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.9 Å
skewness	0.218
kurtosis	-0.645
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	74630000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.185

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.170 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.17 Å
resolution_method	—
num_particles	466159

description	Isoform 1 of Immunoglobulin heavy constant mu
formula_weight	41164.0 kDa
src_method	man
entity_count	12

Cryo-EM structure of the human IgM-Fc hexamer

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

type	polypeptide(L)
strand_id	C,D,K,L,J,I,H,G,E,F,B,A
atom_count	19980

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

fit	/app/data/saxs_computation/uo/9uo3/9uo3.fit
pddf	/app/data/pr_computation/uo/9uo3/9uo3.pr.out
profile	/app/data/saxs_computation/uo/9uo3/9uo3.dat