8equ

Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc

Method: ELECTRON MICROSCOPY D_max: 87.0 Å Quality: REASONABLE

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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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–275 Chain B； UniProt 1–275	Not recorded	Saposin-A × 2 （P07602） Saposin A, polyalanine model × 4 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

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 8EQU	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 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	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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
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

Saposin-A

Homo sapiens

UniProt P07602

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain C； UniProt 60–140 Chain F； UniProt 60–140	Not recorded	ORF3a protein × 2 （P0DTC3） Saposin A, polyalanine model × 4 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8EQU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M12 NMR solution structure of human Saposin C Deposited 2002-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 311–390（80 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) ~10-20mM NaCl；Pressure ambient NMR sample composition U-15N \| 90% H20, 10% D20 NMR sample composition U-15N, U-13C \| 90% H20, 10% D20 NMR sample composition U-15N, U-13C \| 100% D20	Resolution not provided
1N69 Crystal structure of human saposin B Deposited 2002-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–273（79 aa） Chain B 195–273（79 aa）	Not recorded	3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% HYDROGEN PEROXIDE PRIOR TO FREEZING.	Resolution 2.20 Å R-free 0.262
1N69 Crystal structure of human saposin B Deposited 2002-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 195–273（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% HYDROGEN PEROXIDE PRIOR TO FREEZING.	Resolution 2.20 Å R-free 0.262
1SN6 NMR solution structure of human Saposin C in SDS micelles Deposited 2004-03-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 311–390（80 aa） Fragment：Saposin C	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide；Pressure ambient NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide；Pressure ambient NMR sample composition 1mM saposin C U-15N, U-13C; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 90% H20, 10% D20 \| 90% H20, 10% D20 NMR sample composition 1mM saposin C U-15N; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 90% H20, 10% D20 \| 90% H20, 10% D20 NMR sample composition 1mM saposin C U-15N, U-13C; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 100% D20 \| 100% D20	Resolution not provided
2DOB Crystal Structure of Human Saposin A Deposited 2006-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–140（81 aa） Fragment：Saposin A, residues 60-140	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 8K, Calcium Acetate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267
2DOB Crystal Structure of Human Saposin A Deposited 2006-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 60–140（81 aa） Fragment：Saposin A, residues 60-140	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 8K, Calcium Acetate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267
2GTG Crystal Structure of Human Saposin C Deposited 2006-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 311–391（81 aa） Fragment：saposin C, residues 311-391	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG400, Calcium Chloride, Sodium Hepes, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.283
2QYP Orthorhombic Crystal Structure of Human Saposin C Dimer in Open Conformation Deposited 2007-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 311–392（82 aa） Fragment：Saposin-C Domain Chain B 311–392（82 aa） Fragment：Saposin-C Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；20 mM NaAcetate, 200 mM ammonium sulfate, 30% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.45 Å R-free 0.290
2R0R Crystal Structure of Human Saposin D variant SapD K9E Deposited 2007-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–484（78 aa） Chain B 407–484（78 aa）	Mutation：K9E Mutation：K9E	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.287
2R1Q Crystal Structure of Iodinated Human Saposin D in Space Group C2221 Deposited 2007-08-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–484（78 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K	Resolution 2.50 Å R-free 0.278
2RB3 Crystal Structure of Human Saposin D Deposited 2007-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–484（78 aa） Chain D 407–484（78 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K	Resolution 2.10 Å R-free 0.274
2RB3 Crystal Structure of Human Saposin D Deposited 2007-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 407–484（78 aa） Chain C 407–484（78 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K	Resolution 2.10 Å R-free 0.274
2Z9A Crystal Structure of Human Saposin C Dimer in Open Conformation Deposited 2007-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 311–389（79 aa） Chain B 311–389（79 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；20 mM NaAcetate, 240 mM magnesium sulfate, 41% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, vapor diffusion, sitting drop, temperature 291K	Resolution 2.50 Å R-free 0.271
3BQP Crystal Structure of Human Saposin D (orthorhombic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 8K, MAGNESIUM CHLORIDE, TRIS.HCL BUFFER, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.30 Å R-free 0.234
3BQP Crystal Structure of Human Saposin D (orthorhombic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 8K, MAGNESIUM CHLORIDE, TRIS.HCL BUFFER, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.30 Å R-free 0.234
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
3BQQ Crystal Structure of Human Saposin D (triclinic) Deposited 2007-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 405–484（80 aa） Fragment：SAPOSIN D, RESIDUES 405-484	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.242
4DDJ Crystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO) Deposited 2012-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 60–140（81 aa） Fragment：UNP residues 60-140	Not recorded	LDA LAURYL DIMETHYLAMINE-N-OXIDE × 40	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；300 K；1.6 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 300K	Resolution 1.90 Å R-free 0.280
4UEX Structure of human Saposin A at lysosomal pH Deposited 2014-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–142（83 aa） Fragment：RESIDUES 60-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；SITTING-DROP VAPOUR DIFFUSION: 400 NL DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED AGAINST A 80 UL RESERVOIR OF 0.2 M LITHIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.8 AND 25% W/V POLYETHYLENE GLYCOL 4000	Resolution 1.80 Å R-free 0.210
4UEX Structure of human Saposin A at lysosomal pH Deposited 2014-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 60–142（83 aa） Fragment：RESIDUES 60-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；SITTING-DROP VAPOUR DIFFUSION: 400 NL DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED AGAINST A 80 UL RESERVOIR OF 0.2 M LITHIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.8 AND 25% W/V POLYETHYLENE GLYCOL 4000	Resolution 1.80 Å R-free 0.210
4V2O Structure of saposin B in complex with chloroquine Deposited 2014-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–273（79 aa） Chain C 195–273（79 aa）	Not recorded	CLQ N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES, PH 6.0, 30% PEG6000	Resolution 2.13 Å R-free 0.254
4V2O Structure of saposin B in complex with chloroquine Deposited 2014-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 195–273（79 aa）	Not recorded	CLQ N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES, PH 6.0, 30% PEG6000	Resolution 2.13 Å R-free 0.254
6SLR Structure of saposin B in complex with atovaquone Deposited 2019-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–272（78 aa） Chain C 195–272（78 aa）	Not recorded	GOL GLYCEROL × 1 AOQ 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES, 30% PEG6000	Resolution 2.38 Å R-free 0.278
6SLR Structure of saposin B in complex with atovaquone Deposited 2019-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 195–272（78 aa）	Not recorded	GOL GLYCEROL × 4 AOQ 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES, 30% PEG6000	Resolution 2.38 Å R-free 0.278
9AVS Human alpha-galactosidase A in complex with saposin B Deposited 2024-03-04	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 × 3 PDB declaration: trimeric	Chain C 195–273（79 aa）	Not recorded	SO4 SULFATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；500 nL of protein (0.1 mM GLA plus 0.22 mM SapB) was mixed with 500 nL of reservoir solution (0.1 M Tris pH 8.0, 1 M Ammonium sulfate) and equilibrated against 70 uL reservoirs at 20 C.	Resolution 3.53 Å R-free 0.265
9AXG Human saposin B in the presence of globotriaosylceramide-NBD Deposited 2024-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 195–273（79 aa） Chain B 195–273（79 aa）	Not recorded	MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；500 nL of protein-lipid complex (0.82 mM SapB plus 0.87 mM Gb3-NBD) was mixed with 250 nL of reservoir solution (3.1-3.3 M malonate pH 5) and equilibrated against 70 uL reservoirs at 20 C.	Resolution 2.68 Å R-free 0.287
9EKO A chimeric hybrid protein fused with the FGFR3 Transmembrane Domain Deposited 2024-12-03	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 79–139（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.287
9I63 Synthetic Human Saposin D glycoprotein Deposited 2025-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–486（82 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M (NH4)2SO4, 0.2 M NH4OAc, 20 mM Tris pH 7.5	Resolution 1.65 Å R-free 0.201
9I63 Synthetic Human Saposin D glycoprotein Deposited 2025-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 405–486（82 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M (NH4)2SO4, 0.2 M NH4OAc, 20 mM Tris pH 7.5	Resolution 1.65 Å R-free 0.201

20 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 26–106； UniProt 60–140 Author chain F； PDBConstruct 26–106； UniProt 60–140

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8equ
Deposition date deposition_date	2022-10-09
最后修订 last_revision	2023-02-08
Structure title title	Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A 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	31.38 Å
Radius of gyration Rg (electron density) rg_electron	29.52 Å
Forward intensity I(0) i0	115144000.00
Molecular weight molecular_weight	81563.0 kDa
Excluded volume excluded_volume	101160 Å³
Envelope volume envelope_volume	164780 Å³
Hydration-shell volume shell_volume	45369 Å³
Envelope diameter envelope_diameter	86.9 Å
Shell Rg shell_rg	37.98 Å
Envelope Rg envelope_rg	28.82 Å
Shape Rg shape_rg	29.60 Å
Total Rg total_rg	30.26 Å
Total atoms total_atoms	5764
Residues n_residues	858
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	87.0 Å
Rg (real space) rg_real	31.11 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.1510e+08
I(0) uncertainty (real space) i0_real_error	1.5230e+06
Rg (reciprocal space) rg_reciprocal	31.23 Å
I(0) (reciprocal space) i0_reciprocal	115200000.0000
Solution quality estimate total_estimate	0.6909
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.0 Å
Skewness Skewness skewness	-0.007
Kurtosis Kurtosis kurtosis	-0.603
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8370000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.992; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.995; Smooth: 0.500

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5764

MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPLGGRGLEVLFQGPGSGQLVGSGGLEGGGGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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

Entity 2 Entity 2 polymer

Description description	Saposin-A
Molecular weight formula_weight	11677.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MGGHHHHHHSSGVDLGTENLYFQSMSLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCES

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	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Saposin A, polyalanine model
Molecular weight formula_weight	6741.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,G,H

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

来源 Source

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

Entity 4 Entity 4 non-polymer

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	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	2.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	135280

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

Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A 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

Saposin-A

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 (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 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)