SAXSdb — 9r2e

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 1 of Immunoglobulin heavy constant alpha 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain P； UniProt 123–335 Chain Q； UniProt 123–335	Not recorded	ARGX-121 Fab fragment heavy chain × 2 ARGX-121 Fab fragment light chain × 2 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 5 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；16% (w/v) PEG8000, 20% (v/v) Glycerol, 0.16 M MgAcetate, 0.08 M Na Cacodylate pH 6.50	Resolution 2.54 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9R2E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IGA MODEL OF HUMAN IGA1 DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING Deposited 1998-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–353（353 aa） Fragment：CHAINS A AND B, HEAVY, CHAINS C AND D, LIGHT Chain B 1–353（353 aa） Fragment：CHAINS A AND B, HEAVY, CHAINS C AND D, LIGHT	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
1OW0 Crystal structure of human FcaRI bound to IgA1-Fc Deposited 2003-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 122–335（214 aa） Fragment：Fc region Chain B 122–335（214 aa） Fragment：Fc region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；magnesium sulfate heptahydrate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.10 Å R-free 0.284
1OW0 Crystal structure of human FcaRI bound to IgA1-Fc Deposited 2003-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 122–335（214 aa） Fragment：Fc region Chain B 122–335（214 aa） Fragment：Fc region	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；magnesium sulfate heptahydrate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.10 Å R-free 0.284
2QEJ Crystal structure of a Staphylococcus aureus protein (SSL7) in complex with Fc of human IgA1 Deposited 2007-06-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: pentameric	Chain A 123–336（214 aa） Fragment：FC REGION Chain B 123–336（214 aa） Fragment：FC REGION	Not recorded	GOL GLYCEROL × 5 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；12% PEG 8000, 66 mM sodium cacodylate pH 6.5, 130 mM calcium acetate, VAPOR DIFFUSION, temperature 291K	Resolution 3.20 Å R-free 0.312
2QTJ Solution structure of human dimeric immunoglobulin A Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa）	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
2QTJ Solution structure of human dimeric immunoglobulin A Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–475（475 aa） Chain D 1–475（475 aa）	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
3CHN Solution structure of human secretory IgA1 Deposited 2008-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–353（353 aa） Chain B 1–353（353 aa） Chain C 1–353（353 aa） Chain D 1–353（353 aa）	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
6LX3 Cryo-EM structure of human secretory immunoglobulin A Deposited 2020-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 122–353（232 aa） Chain B 122–353（232 aa） Chain C 122–353（232 aa） Chain D 122–353（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
6LXW Cryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal domain of SpsA Deposited 2020-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 122–353（232 aa） Chain B 122–353（232 aa） Chain C 122–353（232 aa） Chain D 122–353（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
6UE7 Structure of dimeric sIgA complex Deposited 2019-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 123–353（231 aa） Fragment：UNP residues 123-353 Chain B 123–353（231 aa） Fragment：UNP residues 123-353 Chain F 123–353（231 aa） Fragment：UNP residues 123-353 Chain G 123–353（231 aa） Fragment：UNP residues 123-353	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6XJA Streptococcus Pneumoniae IgA1 Protease with IgA1 substrate Deposited 2020-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 122–331（210 aa） Chain B 122–331（210 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM Hepes, pH 7 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7UVL IgA1 Protease with IgA1 substrate Deposited 2022-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 123–331（209 aa） Chain B 123–331（209 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
8SKU Structure of human SIgA1 in complex with human CD89 (FcaR1) Deposited 2023-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–353（353 aa） Chain B 1–353（353 aa） Chain C 1–353（353 aa） Chain D 1–353（353 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8SKV Structure of human SIgA1 in complex with Streptococcus pyogenes protein M4 (Arp4) Deposited 2023-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–353（353 aa） Chain B 1–353（353 aa） Chain C 1–353（353 aa） Chain D 1–353（353 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9MBZ Cryo-EM structure of human FcRL4 bound to IgA-Fc/J Deposited 2025-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 122–353（232 aa） Chain B 122–353（232 aa） Chain C 122–353（232 aa） Chain D 122–353（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.30 Å
9OFR CRYSTAL STRUCTURE OF THE HUMAN IGA1 FC FRAGMENT-FC-ALPHA RECEPTOR (CD89) COMPLEX Deposited 2025-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 123–335（213 aa） Fragment：FC fragment, UNP residues 123-335 Chain B 123–335（213 aa） Fragment：FC fragment, UNP residues 123-335	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.15M sodium chloride 0.1M Tris-HCl pH 8.0 8% PEG 6000	Resolution 2.65 Å R-free 0.264
9OFR CRYSTAL STRUCTURE OF THE HUMAN IGA1 FC FRAGMENT-FC-ALPHA RECEPTOR (CD89) COMPLEX Deposited 2025-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 123–335（213 aa） Fragment：FC fragment, UNP residues 123-335 Chain G 123–335（213 aa） Fragment：FC fragment, UNP residues 123-335	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.15M sodium chloride 0.1M Tris-HCl pH 8.0 8% PEG 6000	Resolution 2.65 Å R-free 0.264

14 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGHA1_HUMAN
Isoform	P01876-1
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–213； UniProt 123–335 Author chain Q； PDBConstruct 1–213； UniProt 123–335

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9r2e
Deposition date deposition_date	2025-04-30
最后修订 last_revision	2025-05-14
Structure title title	Structure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1
Keywords keywords	Antibody, immune system, IgA mediated autoimmunity, immunoglobulin, PROTEROS BIOSTRUCTURES GMBH; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	48.93 Å
Radius of gyration Rg (electron density) rg_electron	50.11 Å
Forward intensity I(0) i0	286749000.00
Molecular weight molecular_weight	137470.0 kDa
Excluded volume excluded_volume	171460 Å³
Envelope volume envelope_volume	250300 Å³
Hydration-shell volume shell_volume	47226 Å³
Envelope diameter envelope_diameter	187.3 Å
Shell Rg shell_rg	45.26 Å
Envelope Rg envelope_rg	50.30 Å
Shape Rg shape_rg	50.04 Å
Total Rg total_rg	50.11 Å
Total atoms total_atoms	9665
Residues n_residues	1283
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	176.0 Å
Rg (real space) rg_real	49.92 Å
Rg uncertainty (real space) rg_real_error	2.31 Å
I(0) (real space) i0_real	2.8670e+08
I(0) uncertainty (real space) i0_real_error	5.3650e+06
Rg (reciprocal space) rg_reciprocal	48.94 Å
I(0) (reciprocal space) i0_reciprocal	286400000.0000
Solution quality estimate total_estimate	0.5274
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.643
Kurtosis Kurtosis kurtosis	-0.116
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17180000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.650; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.528; Smooth: 0.335

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	ARGX-121 Fab fragment heavy chain
Molecular weight formula_weight	25904.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A
Atom count atom_count	10097

MGWSCIILFLVATATGVHSEVQLLESGGGLVQPGGSLRLSCAASGFTSSNYLMSWVRQAPGKGLEWVSSIYHYGHNAYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVDSAYDFGSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	ARGX-121 Fab fragment light chain
Molecular weight formula_weight	24725.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,B

MGWSCIILFLVATATGVHSQSVLTQPPSVSGAPGQRVTISCAGTSSDIGGRTYVSWYQQLPGTAPKLLIYKVTIRASGVPDRFSGSKSGTSASLAITGLQAEDEADYYCASHRSNNNIVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Isoform 1 of Immunoglobulin heavy constant alpha 1
Molecular weight formula_weight	23155.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

CHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLCGCYSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEELALNELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVAAEDWKKGDTFSCMVGHEALPLAFTQKTIDRLAGK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	377

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8. Citations (1)

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Unit-cell length a length_a	77.291 Å
Unit-cell length b length_b	232.312 Å
Unit-cell length c length_c	105.519 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.540 Å
Low-resolution limit resolution_low	116.160 Å
R factor r_factor	0.2131
R_work r_work	0.2109
R_free r_free	0.2518

fit	/app/data/saxs_computation/r2/9r2e/9r2e.fit
pddf	/app/data/pr_computation/r2/9r2e/9r2e.pr.out
profile	/app/data/saxs_computation/r2/9r2e/9r2e.dat

Structure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 1 of Immunoglobulin heavy constant alpha 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)