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9t5z

Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain)

Method: ELECTRON MICROSCOPY D_max: 129.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t5z
deposition_date	2025-11-06
title	Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain)
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	40.85 Å
rg_electron	40.24 Å
i0	365329000.00
molecular_weight	153070.0 kDa
excluded_volume	190160 Å³
envelope_volume	260870 Å³
shell_volume	52867 Å³
envelope_diameter	126.3 Å
shell_rg	46.85 Å
envelope_rg	39.74 Å
shape_rg	40.19 Å
total_rg	40.73 Å
total_atoms	21176
n_residues	1363
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	129.8 Å
rg_real	40.76 Å
rg_real_error	1.12 Å
i0_real	3.6530e+08
i0_real_error	5.1960e+06
rg_reciprocal	40.85 Å
i0_reciprocal	365400000.0000
total_estimate	0.9039
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	46.6 Å
skewness	0.134
kurtosis	-0.733
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	43390000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.911

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Integrin alpha-M
formula_weight	83912.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	21183

FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPIRLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQKFPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFRITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAGGVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFRQNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPLPRGRTRWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFHGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQPVLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVTYDLALDSGRPHSRAVFNETKRSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNFSLVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNTGGLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Integrin beta-2
formula_weight	52217.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEPAALQTLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Murine IgG1 MEM148 heavy chain
formula_weight	23865.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPYNKLEYMGYISYSGSTYYNPSLESRVSITRDTSKNQYYLQLHSVTTEDTATYHCARERDYAFDFWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 4 polymer

description	Anti-colorectal carcinoma light chain
formula_weight	23936.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIKMTQSPSPMYASLGERVTVTCKASQDINNYLSWFQQKPGKSPKTLIYRAKRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 5 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 6 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 7 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 8 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	5

Entity 9 non-polymer

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

Entity 10 non-polymer

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

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	7

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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	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	188421

fit	/app/data/saxs_computation/t5/9t5z/9t5z.fit
pddf	/app/data/pr_computation/t5/9t5z/9t5z.pr.out
profile	/app/data/saxs_computation/t5/9t5z/9t5z.dat

Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain)

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 (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)