SAXSdb — 9ru5

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

MHC class I antigen

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain M； UniProt 27–302	Not recorded	TCRpub alpha chain × 1 TCRpub beta chain × 1 ORF3a protein × 1 （P0DTC3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；30 mM HEPES pH 7.4, 150 mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.26 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 9RU5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8T7R Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of alloreactive antibody E07 Deposited 2023-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 50 PDB declaration: 50-meric	Chain C 25–298（274 aa） Chain G 25–298（274 aa） Chain K 25–298（274 aa） Chain O 25–298（274 aa） Chain S 25–298（274 aa） Chain W 25–298（274 aa） Chain a 25–298（274 aa） Chain e 25–298（274 aa） Chain i 25–298（274 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；sodium citrate tribasic dihydrate, sodium cacodylate	Resolution 3.84 Å R-free 0.263
8YIV N17.1.2 recognition of NRAS neoantigens Deposited 2024-02-29	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 25–299（275 aa）	Not recorded	GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10mg/ml, 8% TacsimateTM pH7.0, 20% PEG4K	Resolution 2.10 Å R-free 0.226
8YJ2 N17.1.2 recognition of NRAS neoantigens Deposited 2024-02-29	Different construct 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, HANGING DROP；293 K；10mg/ml, 0.2 M NH4 citrate tribasic, 16% PEG3350, pH 7.4	Resolution 2.26 Å R-free 0.229

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F6IQR9_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–276； UniProt 27–302

ORF3a protein

Severe acute respiratory syndrome coronavirus 2

UniProt P0DTC3

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain P； UniProt 207–215	Not recorded	TCRpub alpha chain × 1 TCRpub beta chain × 1 MHC class I antigen × 1 （F6IQR9）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；30 mM HEPES pH 7.4, 150 mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.26 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 9RU5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XDC Cryo-EM structure of SARS-CoV-2 ORF3a Deposited 2020-06-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa） Chain B 1–275（275 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；1 blot force, 5 second wait time, 3 second blot time	Resolution 2.90 Å
7KJR Cryo-EM structure of SARS-CoV-2 ORF3a Deposited 2020-10-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–275（275 aa） Chain B 1–275（275 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；1 blot force 5 second wait time 3 second blot time	Resolution 2.08 Å
8EQJ Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like membrane environment, MSP1D1 nanodisc Deposited 2022-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa） Chain B 1–275（275 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8EQT Structure of SARS-CoV-2 Orf3a in plasma membrane-like environment, MSP1D1 nanodisc Deposited 2022-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa） Chain B 1–275（275 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8EQU Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc Deposited 2022-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–275（275 aa） Chain B 1–275（275 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8T5P SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain Deposited 2023-06-14	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 G 36–40（5 aa） Fragment：UNP residues 36-40 Chain H 36–40（5 aa） Fragment：UNP residues 36-40	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate	Resolution 2.50 Å R-free 0.242
8T5P SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain Deposited 2023-06-14	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 36–40（5 aa） Fragment：UNP residues 36-40	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate	Resolution 2.50 Å R-free 0.242
8T5Q SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain Deposited 2023-06-14	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 G 36–40（5 aa） Fragment：UNP residues 36-40 Chain H 36–40（5 aa） Fragment：UNP residues 36-40	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277.15 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000	Resolution 1.90 Å R-free 0.240
8T5Q SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain Deposited 2023-06-14	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 36–40（5 aa） Fragment：UNP residues 36-40	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277.15 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000	Resolution 1.90 Å R-free 0.240

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AP3A_SARS2
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–9； UniProt 207–215

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	9ru5
Deposition date deposition_date	2025-07-03
Structure title title	Cryo-EM structure of TCRpub/pMHC
Keywords keywords	complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	29.66 Å
Radius of gyration Rg (electron density) rg_electron	28.96 Å
Forward intensity I(0) i0	79409500.00
Molecular weight molecular_weight	68363.0 kDa
Excluded volume excluded_volume	84662 Å³
Envelope volume envelope_volume	107770 Å³
Hydration-shell volume shell_volume	31843 Å³
Envelope diameter envelope_diameter	96.6 Å
Shell Rg shell_rg	35.53 Å
Envelope Rg envelope_rg	28.97 Å
Shape Rg shape_rg	28.95 Å
Total Rg total_rg	29.62 Å
Total atoms total_atoms	4825
Residues n_residues	605
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	97.5 Å
Rg (real space) rg_real	29.75 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	7.9410e+07
I(0) uncertainty (real space) i0_real_error	1.3450e+06
Rg (reciprocal space) rg_reciprocal	29.72 Å
I(0) (reciprocal space) i0_reciprocal	79410000.0000
Solution quality estimate total_estimate	0.8876
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.504
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15520000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	TCRpub alpha chain
Molecular weight formula_weight	23175.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4825

QSVAQPEDQVNVAEGNPLTVKCTYSVSGNPYLFWYVQYPNRGLQFLLKYITGDNLVKGSYGFEAEFNKSQTSFHLKKPSALVSDSALYFCAVRVVTSGGSYIPTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

来源 Source

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

Entity 2 Entity 2 polymer

Description description	TCRpub beta chain
Molecular weight formula_weight	27151.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLAGDLGTEAFFGQGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

来源 Source

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

Entity 3 Entity 3 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	31909.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSS

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 polymer

Description description	ORF3a protein
Molecular weight formula_weight	1199.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

FTSDYYQLY

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
通用名 common_name	2019-nCoV, SARS-CoV-2
NCBI Class编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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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	—

Resolution resolution	3.260 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.26 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	103583

fit	/app/data/saxs_computation/ru/9ru5/9ru5.fit
pddf	/app/data/pr_computation/ru/9ru5/9ru5.pr.out
profile	/app/data/saxs_computation/ru/9ru5/9ru5.dat

Cryo-EM structure of TCRpub/pMHC

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

MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

ORF3a protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)