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9t3y

Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)

Method: ELECTRON MICROSCOPY D_max: 203.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t3y
deposition_date	2025-10-30
title	Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)
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	57.77 Å
rg_electron	58.90 Å
i0	516883000.00
molecular_weight	184240.0 kDa
excluded_volume	229150 Å³
envelope_volume	338080 Å³
shell_volume	56672 Å³
envelope_diameter	226.8 Å
shell_rg	46.93 Å
envelope_rg	60.61 Å
shape_rg	58.82 Å
total_rg	58.72 Å
total_atoms	12928
n_residues	1632
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	203.6 Å
rg_real	58.66 Å
rg_real_error	2.29 Å
i0_real	5.1680e+08
i0_real_error	1.1670e+07
rg_reciprocal	56.99 Å
i0_reciprocal	515500000.0000
total_estimate	0.7683
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.7 Å
skewness	0.624
kurtosis	-0.085
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0007
highest_alpha	17020000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.651; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.476; Smooth: 0.556

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

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	12937

FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPIRLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQKFPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAGGVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFRQNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPLPRGQRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFHGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQPVLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVTYDLALDSGRPHSRAVFNETKNSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNFSLVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNTGGENLYFQ

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Integrin beta-2
formula_weight	52281.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEPAAENLYFQ

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Nanobody,Complement C3dg fragment
formula_weight	49171.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QVQLVESGGGLVQAGGSLRLSCTTSGFTFDDYAIGWFRQAPGKEREGVSCISSSEGKYYSDGGGGSGGGGSGGGGSVDAERLKHLIVTPSGSGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHKGGGGSGRFTISSDNAKNTVYLQMNNLKPEDTAVYYCAAEWNNFGRLCMYPDYWGQGTQVTVSSENLYFQGHHHHHH

Source

organism	Lama glama
common_name	llama
ncbi_taxonomy_id	9844
host_organism	Homo sapiens

Entity 4 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 5 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	2

Entity 6 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	2

Entity 7 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	5

Entity 8 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	9

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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	3.440 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.44 Å
resolution_method	—
num_particles	43930

fit	/app/data/saxs_computation/t3/9t3y/9t3y.fit
pddf	/app/data/pr_computation/t3/9t3y/9t3y.pr.out
profile	/app/data/saxs_computation/t3/9t3y/9t3y.dat

Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)

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 (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)