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9td2

Integrin AlphaIIbBeta3 bound to Fab of the anti-HPA-1a antibody 26.4

Method: ELECTRON MICROSCOPY D_max: 177.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9td2
deposition_date	2025-11-22
title	Integrin AlphaIIbBeta3 bound to Fab of the anti-HPA-1a antibody 26.4
keywords	Human Platelet Antigen, FNAIT, alloantibody, cryo-EM, CELL ADHESION; CELL ADHESION
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	51.07 Å
rg_electron	52.06 Å
i0	518210000.00
molecular_weight	182080.0 kDa
excluded_volume	225200 Å³
envelope_volume	324080 Å³
shell_volume	57224 Å³
envelope_diameter	189.8 Å
shell_rg	48.94 Å
envelope_rg	51.21 Å
shape_rg	52.11 Å
total_rg	51.81 Å
total_atoms	24998
n_residues	1643
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	177.0 Å
rg_real	51.62 Å
rg_real_error	2.28 Å
i0_real	5.1820e+08
i0_real_error	1.0440e+07
rg_reciprocal	50.61 Å
i0_reciprocal	517500000.0000
total_estimate	0.7553
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.0 Å
skewness	0.628
kurtosis	-0.259
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	35960000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.567; Smooth: 0.201

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Integrin alpha-IIb
formula_weight	108456.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	25007

LNLDPVQLTFYAGPNGSQFGFSLDFHKDSHGRVAIVVGAPRTLGPSQEETGGVFLCPWRAEGGQCPSLLFDLRDETRNVGSQTLQTFKARQGLGASVVSWSDVIVACAPWQHWNVLEKTEEAEKTPVGSCFLAQPESGRRAEYSPCRGNTLSRIYVENDFSWDKRYCEAGFSSVVTQAGELVLGAPGGYYFLGLLAQAPVADIFSSYRPGILLWHVSSQSLSFDSSNPEYFDGYWGYSVAVGEFDGDLNTTEYVVGAPTWSWTLGAVEILDSYYQRLHRLRGEQMASYFGHSVAVTDVNGDGRHDLLVGAPLYMESRADRKLAEVGRVYLFLQPRGPHALGAPSLLLTGTQLYGRFGSAIAPLGDLDRDGYNDIAVAAPYGGPSGRGQVLVFLGQSEGLRSRPSQVLDSPFPTGSAFGFSLRGAVDIDDNGYPDLIVGAYGANQVAVYRAQPVVKASVQLLVQDSLNPAVKSCVLPQTKTPVSCFNIQMCVGATGHNIPQKLSLNAELQLDRQKPRQGRRVLLLGSQQAGTTLNLDLGGKHSPICHTTMAFLRDEADFRDKLSPIVLSLNVSLPPTEAGMAPAVVLHGDTHVQEQTRIVLDCGEDDVCVPQLQLTASVTGSPLLVGADNVLELQMDAANEGEGAYEAELAVHLPQGAHYMRALSNVEGFERLICNQKKENETRVVLCELGNPMKKNAQIGIAMLVSVGNLEEAGESVSFQLQIRSKNSQNPNSKIVLLDVPVRAEAQVELRGNSFPASLVVAAEEGEREQNSLDSWGPKVEHTYELHNNGPGTVNGLHLSIHLPGQSQPSDLLYILDIQPQGGLQCFPQPPVNPLKVDWGLPIPSPSPIHPAHHKRDRRQIFLPEPEQPSRLQDPVLVSCDSAPCTVVQCDLQEMARGQRAMVTVLAFLWLPSLYQRPLDQFVLQSHAWFNVSSLPYAVPPLSLPRGEAQVWTQLLRALEERAAQCEKELQALEKENAQLEWELQALEKELAQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 polymer

description	Integrin beta-3
formula_weight	81402.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSEARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEKCPTCPDACTFKKECVECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAVNCTYKNEDDCVVRFQYYEDSSGKSILYVVEEPECPKGPDGGLENLYFQGGKNAQCKKKLQALKKKNAQLKWKLQALKKKLAQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	Antibody 26.4 Fab heavy chain
formula_weight	26033.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLQQSGPGLVKPSQTLSLTCAISGDSVSSNSAAWNWIRQSPSRGLEWLGRTYFRSNWYNDYAASVKSRITINQDTSKNQLSLQLNSVTPEDTAMYYCARDGAWGGSSWWPGLPHHYYSGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Antibody 26.4 Fab light chain
formula_weight	23441.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASKRATGIPARFSGSGSGTDFSLTIRSLEPEDFAVYYCQQRSDWQGLTFGGGTKVEIKTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 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 6 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	1

Entity 7 branched

description	alpha-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	2

Entity 8 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	6

Entity 9 non-polymer

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

Entity 10 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 11 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	triclinic

resolution	2.640 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.64 Å
resolution_method	—
num_particles	84349

fit	/app/data/saxs_computation/td/9td2/9td2.fit
pddf	/app/data/pr_computation/td/9td2/9td2.pr.out
profile	/app/data/saxs_computation/td/9td2/9td2.dat

Integrin AlphaIIbBeta3 bound to Fab of the anti-HPA-1a antibody 26.4

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)