SAXSdb — 8eqt

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

ORF3a protein

Severe acute respiratory syndrome coronavirus 2

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–275 Chain B； UniProt 1–275	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

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 8EQT	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 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	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 oligomeric state 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 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
8EQU Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc Deposited 2022-10-09	Different oligomeric state Different ligand/ion 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 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	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 mutation/modification 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 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 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 mutation/modification 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 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
9RU5 Cryo-EM structure of TCRpub/pMHC Deposited 2025-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 207–215（9 aa）	Not recorded	No recorded non-water small molecule	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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–275； UniProt 1–275 Author chain B； PDBConstruct 1–275； UniProt 1–275

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	8eqt
Deposition date deposition_date	2022-10-09
Structure title title	Structure of SARS-CoV-2 Orf3a in plasma membrane-like environment, MSP1D1 nanodisc
Keywords keywords	Membrane protein, SARS-CoV-2, VIRAL PROTEIN; VIRAL PROTEIN
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	23.93 Å
Radius of gyration Rg (electron density) rg_electron	23.76 Å
Forward intensity I(0) i0	29872000.00
Molecular weight molecular_weight	45379.0 kDa
Excluded volume excluded_volume	58146 Å³
Envelope volume envelope_volume	69320 Å³
Hydration-shell volume shell_volume	25182 Å³
Envelope diameter envelope_diameter	83.2 Å
Shell Rg shell_rg	30.19 Å
Envelope Rg envelope_rg	23.96 Å
Shape Rg shape_rg	23.80 Å
Total Rg total_rg	24.44 Å
Total atoms total_atoms	3206
Residues n_residues	382
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	82.0 Å
Rg (real space) rg_real	24.05 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	2.9870e+07
I(0) uncertainty (real space) i0_real_error	3.8040e+05
Rg (reciprocal space) rg_reciprocal	24.02 Å
I(0) (reciprocal space) i0_reciprocal	29870000.0000
Solution quality estimate total_estimate	0.8571
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.540
Kurtosis Kurtosis kurtosis	-0.046
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6792000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (2)

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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	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	125625

Description description	ORF3a protein
Molecular weight formula_weight	36489.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3206

Structure of SARS-CoV-2 Orf3a in plasma membrane-like environment, MSP1D1 nanodisc

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

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	4

fit	/app/data/saxs_computation/eq/8eqt/8eqt.fit
pddf	/app/data/pr_computation/eq/8eqt/8eqt.pr.out
profile	/app/data/saxs_computation/eq/8eqt/8eqt.dat