SAXSdb — 8esa

▼

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

Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 25–300 Chain B； UniProt 25–300 Chain C； UniProt 25–300	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

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 8ESA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TO2 Structure of HLA-A*0201 complexed with peptide Md3-C9 derived from a clustering region of restricted cytotoxic T lymphocyte epitope from SARS-CoV M protein Deposited 2011-09-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–299（275 aa） Fragment：UNP residues 25-299	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Ammonium acetate, 0.1M BIS-Tris pH6.5, 17% polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.230
7RTD SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01 Deposited 2021-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2M NaFluoride	Resolution 2.05 Å R-free 0.235
7RTR YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01 Deposited 2021-08-14	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 × 5 PDB declaration: pentameric	Chain A 1–365（365 aa）	Not recorded	NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.05 M Zinc Acetate	Resolution 2.60 Å R-free 0.235
7U1R SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by HLA-A*02:01 Deposited 2022-02-22	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 × 3 PDB declaration: trimeric	Chain A 1–365（365 aa）	Not recorded	CD CADMIUM ION × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 ACT ACETATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；18% P4000, 0.1M HEPES 7.6, 0.1M MgCl2, 1 mM CdCl2	Resolution 1.80 Å R-free 0.196
7UM2 SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01 Deposited 2022-04-06	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 × 3 PDB declaration: trimeric	Chain A 1–365（365 aa）	Not recorded	ZN ZINC ION × 1 CD CADMIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；14% P3350; 0.1M NaFlu; 2% EG; 1 mM CdCl2	Resolution 1.63 Å R-free 0.195
7UR1 SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01 Deposited 2022-04-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% P3350; 0.2 M K Acet	Resolution 2.17 Å R-free 0.277
8EB2 Structure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2.1 Fab Deposited 2022-08-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 25–299（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M L-Proline, 0.1M HEPES pH 7.5, 13% PEG3350	Resolution 2.90 Å R-free 0.284
8EB2 Structure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2.1 Fab Deposited 2022-08-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 25–299（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M L-Proline, 0.1M HEPES pH 7.5, 13% PEG3350	Resolution 2.90 Å R-free 0.284
8EB2 Structure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2.1 Fab Deposited 2022-08-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 25–299（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M L-Proline, 0.1M HEPES pH 7.5, 13% PEG3350	Resolution 2.90 Å R-free 0.284
8ESB CryoEM structure of HLA-A2 bound to MAGEA8 (232-241) peptide Deposited 2022-10-13	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 25–300（276 aa） Chain B 25–300（276 aa） Chain C 25–300（276 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
8FU4 HCMV US11 peptide binding to HLA-A*02:01 Deposited 2023-01-16	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 × 3 PDB declaration: trimeric	Chain A 25–299（275 aa）	Not recorded	GOL GLYCEROL × 2 CD CADMIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；26% (w/v) PEG3350 and 0.1 M DL-malic acid pH 7.0, 83 mM cesium chloride	Resolution 1.60 Å R-free 0.204
8RBV SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by HLA-A*02:01 Deposited 2023-12-05	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 × 3 PDB declaration: trimeric	Chain A 1–365（365 aa）	Not recorded	ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 2 CD CADMIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；13% P3350; 0.1M NaFlu; 2% EG; 1 mM CdCl2	Resolution 1.80 Å R-free 0.211
8TBV Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL Deposited 2023-06-29	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 × 3 PDB declaration: trimeric	Chain A 25–299（275 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen	Resolution 2.64 Å R-free 0.274
8TBV Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL Deposited 2023-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–299（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen	Resolution 2.64 Å R-free 0.274
8TBW Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) peptide KLSHQPVLL Deposited 2023-06-29	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 × 3 PDB declaration: trimeric	Chain A 25–299（275 aa）	Not recorded	NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen	Resolution 2.08 Å R-free 0.205
8TBW Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) peptide KLSHQPVLL Deposited 2023-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–299（275 aa）	Not recorded	NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen	Resolution 2.08 Å R-free 0.205
8U9G Human Class I MHC HLA-A2 bound to sorting nexin 24 (127-135) neoantigen KLSHQLVLL Deposited 2023-09-19	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 × 3 PDB declaration: trimeric	Chain A 25–299（275 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen	Resolution 2.87 Å R-free 0.245
8U9G Human Class I MHC HLA-A2 bound to sorting nexin 24 (127-135) neoantigen KLSHQLVLL Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–299（275 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen	Resolution 2.87 Å R-free 0.245
9MIN Structure of a designed minibinder to NYESO1-A*02:01 Deposited 2024-12-13	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 × 5 PDB declaration: pentameric	Chain A 24–300（277 aa）	Mutation：insertion of MG at N-terminus - cloning artifact	GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M ammonium acetate 0.1 M bis-tris pH 5.5 25% PEG 3350	Resolution 2.05 Å R-free 0.267
9MIN Structure of a designed minibinder to NYESO1-A*02:01 Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 24–300（277 aa）	Mutation：insertion of MG at N-terminus - cloning artifact	GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M ammonium acetate 0.1 M bis-tris pH 5.5 25% PEG 3350	Resolution 2.05 Å R-free 0.267

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q53Z42_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 145–420； UniProt 25–300 Author chain B； PDBConstruct 145–420； UniProt 25–300 Author chain C； PDBConstruct 145–420； UniProt 25–300

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8esa
Deposition date deposition_date	2022-10-13
Structure title title	CryoEM structure of HLA-A2 bound to MAGEA4 (230-239) peptide
Keywords keywords	HLA, MHC, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.52 Å
Radius of gyration Rg (electron density) rg_electron	23.30 Å
Forward intensity I(0) i0	36386600.00
Molecular weight molecular_weight	44465.0 kDa
Excluded volume excluded_volume	54747 Å³
Envelope volume envelope_volume	70041 Å³
Hydration-shell volume shell_volume	25115 Å³
Envelope diameter envelope_diameter	77.7 Å
Shell Rg shell_rg	30.23 Å
Envelope Rg envelope_rg	23.41 Å
Shape Rg shape_rg	23.27 Å
Total Rg total_rg	24.21 Å
Total atoms total_atoms	3140
Residues n_residues	384
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

▼

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

Maximum dimension Dmax dmax	75.3 Å
Rg (real space) rg_real	24.44 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	3.6390e+07
I(0) uncertainty (real space) i0_real_error	5.2580e+05
Rg (reciprocal space) rg_reciprocal	24.46 Å
I(0) (reciprocal space) i0_reciprocal	36390000.0000
Solution quality estimate total_estimate	0.7135
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8735000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 0.137; Positv: 1.000; Valcen: 0.999; Smooth: 0.974

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	76433

Description description	Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera
Molecular weight formula_weight	50306.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3140

CryoEM structure of HLA-A2 bound to MAGEA4 (230-239) peptide

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

Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Cricetulus griseus

fit	/app/data/saxs_computation/es/8esa/8esa.fit
pddf	/app/data/pr_computation/es/8esa/8esa.pr.out
profile	/app/data/saxs_computation/es/8esa/8esa.dat