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9rma

;Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex ;

Method: ELECTRON MICROSCOPY D_max: 92.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rma
deposition_date	2025-06-18
title	;Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex ;
keywords	phagocytosis, integrin, opsonisation, 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	29.94 Å
rg_electron	29.25 Å
i0	75054100.00
molecular_weight	68318.0 kDa
excluded_volume	85617 Å³
envelope_volume	108510 Å³
shell_volume	31203 Å³
envelope_diameter	98.6 Å
shell_rg	36.15 Å
envelope_rg	29.02 Å
shape_rg	29.23 Å
total_rg	29.98 Å
total_atoms	9555
n_residues	607
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	92.0 Å
rg_real	29.91 Å
rg_real_error	0.69 Å
i0_real	7.5050e+07
i0_real_error	1.2980e+06
rg_reciprocal	29.93 Å
i0_reciprocal	75060000.0000
total_estimate	0.9068
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.5 Å
skewness	0.208
kurtosis	-0.705
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	20280000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.895

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isoform 2 of Integrin alpha-M
formula_weight	83989.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9557

FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPIRLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQKFPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAGGVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFRQNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPLPRGQRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFHGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQPVLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVTYDLALDSGRPHSRAVFNETKNSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNFSLVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNTGGENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	C3d-anti-CR3-Nb fusion ligand
formula_weight	51073.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MGWSCIILFLVATATGVHQVQLVESGGGLVQAGGSLRLSCTTSGFTFDDYAIGWFRQAPGKEREGVSCISSSEGKYYSDGGGGSGGGGSGGGGSVDAERLKHLIVTPSGSGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHKGGGGSGRFTISSDNAKNTVYLQMNNLKPEDTAVYYCAAEWNNFGRLCMYPDYWGQGTQVTVSSENLYFQGHHHHHH

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Lama glama

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2

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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	3.940 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.94 Å
resolution_method	—
num_particles	184079

fit	/app/data/saxs_computation/rm/9rma/9rma.fit
pddf	/app/data/pr_computation/rm/9rma/9rma.pr.out
profile	/app/data/saxs_computation/rm/9rma/9rma.dat

;Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex ;

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)