SAXSdb — 4oq8

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

Coat protein

OrganismNot specified

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–RNA Homooligomer Protein × 60 RNA 180 PDB declaration: 240-meric（240） Consistent with all polymer counts	Chain A； UniProt 1–159	Not recorded	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 60 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 60 ;RNA (5'-R(PUPU)-3') ; × 60 PO4 PHOSPHATE ION × 60 SO4 SULFATE ION × 120 MG MAGNESIUM ION × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.279
2	Protein–RNA Monomer Protein × 1 RNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–159	Not recorded	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 1 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1 ;RNA (5'-R(PUPU)-3') ; × 1 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.279
3	Protein–RNA Homooligomer Protein × 5 RNA 15 PDB declaration: eicosameric（20） Consistent with all polymer counts	Chain A； UniProt 1–159	Not recorded	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 5 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 5 ;RNA (5'-R(PUPU)-3') ; × 5 PO4 PHOSPHATE ION × 5 SO4 SULFATE ION × 10 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.279
4	Protein–RNA Homooligomer Protein × 6 RNA 18 PDB declaration: 24-meric（24） Consistent with all polymer counts	Chain A； UniProt 1–159	Not recorded	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 6 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 6 ;RNA (5'-R(PUPU)-3') ; × 6 PO4 PHOSPHATE ION × 6 SO4 SULFATE ION × 12 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.279
5	Protein–RNA Monomer Protein × 1 RNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–159	Not recorded	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 1 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1 ;RNA (5'-R(PUPU)-3') ; × 1 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.279
6	Protein–RNA Homooligomer Protein × 15 RNA 45 PDB declaration: 60-meric（60） Consistent with all polymer counts	Chain A； UniProt 1–159	Not recorded	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 15 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 15 ;RNA (5'-R(PUPU)-3') ; × 15 PO4 PHOSPHATE ION × 15 SO4 SULFATE ION × 30 MG MAGNESIUM ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.279

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 4OQ8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A34 SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX Deposited 1998-01-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 180-MERIC	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 60 U5P URIDINE-5'-MONOPHOSPHATE × 60	X-RAY DIFFRACTION X-ray crystallization conditions liquid diffusion in microgravity；pH 6.5；PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity	Resolution 1.81 Å R-free 0.184
1A34 SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX Deposited 1998-01-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 1 U5P URIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions liquid diffusion in microgravity；pH 6.5；PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity	Resolution 1.81 Å R-free 0.184
1A34 SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX Deposited 1998-01-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Homooligomer；Protein × 5 PDB declaration: pentadecameric	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 5 U5P URIDINE-5'-MONOPHOSPHATE × 5	X-RAY DIFFRACTION X-ray crystallization conditions liquid diffusion in microgravity；pH 6.5；PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity	Resolution 1.81 Å R-free 0.184
1A34 SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX Deposited 1998-01-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Homooligomer；Protein × 6 PDB declaration: octadecameric	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 6 U5P URIDINE-5'-MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions liquid diffusion in microgravity；pH 6.5；PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity	Resolution 1.81 Å R-free 0.184
1A34 SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX Deposited 1998-01-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 1 U5P URIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions liquid diffusion in microgravity；pH 6.5；PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity	Resolution 1.81 Å R-free 0.184
1A34 SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX Deposited 1998-01-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–RNA Homooligomer；Protein × 15 PDB declaration: 45-meric	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 15 U5P URIDINE-5'-MONOPHOSPHATE × 15	X-RAY DIFFRACTION X-ray crystallization conditions liquid diffusion in microgravity；pH 6.5；PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity	Resolution 1.81 Å R-free 0.184
4NIA Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints Deposited 2013-11-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 240-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	MG MAGNESIUM ION × 12 PO4 PHOSPHATE ION × 12 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 6.5；296 K；9 crystals were grown in microgravity aboard IML-I mission of the U.S. Space Shuttle over 12 days using 20% ammonium sulfate as precipitant, pH 6.50, LIQUID DIFFUSION, temperature 296K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；12 crystals grown from 8% ammonium sulfate on earth with a reservoir of 14-16% ammonium sulfate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.82 Å R-free 0.156
4OQ9 Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints Deposited 2014-02-07	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 240-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 12 SO4 SULFATE ION × 72 NA SODIUM ION × 68 MG MAGNESIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.250
4OQ9 Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints Deposited 2014-02-07	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein–RNA Homooligomer；Protein × 15 PDB declaration: 60-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 3 SO4 SULFATE ION × 18 NA SODIUM ION × 17 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.250
4OQ9 Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints Deposited 2014-02-07	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 3 Protein–RNA Homooligomer；Protein × 15 PDB declaration: 60-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 3 SO4 SULFATE ION × 18 NA SODIUM ION × 17 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.250
4OQ9 Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints Deposited 2014-02-07	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 4 Protein–RNA Homooligomer；Protein × 15 PDB declaration: 60-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 3 SO4 SULFATE ION × 18 NA SODIUM ION × 17 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.45 Å R-free 0.250
5BKL Crystallographic structure of the cubic crystal form of STMV (77.9 degree rotation) grown from NaCl Deposited 2021-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 117-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	CL CHLORIDE ION × 120 MG MAGNESIUM ION × 39	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were composed of equal amounts of a 5 mg/ml stock virus solution buffered at pH6.5 with 0.1 M phosphate, and the reservoir solution which was 8% w/v NaCl buffered with 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.	Resolution 2.94 Å R-free 0.256
5BKN Crystallographic structure of a cubic crystal form of STMV (84.5 degree rotation) grown from chloride Deposited 2021-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 117-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	CL CHLORIDE ION × 78 MG MAGNESIUM ION × 42	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates using .6 ml reservoirs. The drops were composed of equal volumes of a 5 mg/ml virus stock solution of 0.1 M phosphate at pH 6.5, and the reservoir solution, which was 8% NaCl w/v in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C.	Resolution 3.00 Å R-free 0.255
5BKQ Crystallographic structure of a cubic form of STMV grown from nitrate Deposited 2021-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	NO3 NITRATE ION × 306 MG MAGNESIUM ION × 27	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were equal amounts of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH 6.5, and the reservoir solution which was 20% w/v sodium nitrate in 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.	Resolution 3.19 Å R-free 0.273
7M2T Crystallographic Structure of the Monoclinic Form of Satellite Tobacco Mosaic Virus Deposited 2021-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 218-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain BB 1–159（159 aa） Chain C 1–159（159 aa） Chain CC 1–159（159 aa） Chain D 1–159（159 aa） Chain DD 1–159（159 aa） Chain E 1–159（159 aa） Chain EE 1–159（159 aa） Chain F 1–159（159 aa） Chain FF 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain LL 1–159（159 aa） Chain M 1–159（159 aa） Chain MM 1–159（159 aa） Chain N 1–159（159 aa） Chain NN 1–159（159 aa） Chain O 1–159（159 aa） Chain OO 1–159（159 aa） Chain PP 1–159（159 aa）	Not recorded	MG MAGNESIUM ION × 12 PO4 PHOSPHATE ION × 12 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；279 K；Crystals grown by vapor diffusion as sitting drops. Drops were equal volumes of a 6 mg/ml STMV stock solution buffered at pH 6.5 with 0.1 M phosphate. The reservoirs were 16% saturated ammonium sulfate in 0.1 M phosphate at pH 6.5. Drops were 6 to 8 ul with 0.60 ml reservoirs. Crystals were grown at 4 degrees C over a weeks time.	Resolution 2.71 Å R-free 0.177
7M2V Crystallographic Structure of the Rhombohedral Crystal Form of STMV Grown from Chloride Deposited 2021-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 120-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain FX 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain NN 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	CL CHLORIDE ION × 39 MG MAGNESIUM ION × 24 PO4 PHOSPHATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. Drops were equal amounts of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1 M phosphate, and the reservoir solution. The reservoir solution was 4% w/v NaCl in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C.	Resolution 1.80 Å R-free 0.217
7M3R Crystallographic Structure of the Rhombohedral Crystal Form of STMV Grown from Bromide Deposited 2021-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	BR BROMIDE ION × 573 MG MAGNESIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. The drops were equal amounts of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1 M phosphate. The reservoirs were 5% w/v NaBr in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C and the time of development was about 10 days.	Resolution 2.10 Å R-free 0.208
7M3T Crystallographic structure of a cubic crystal of STMV (80.7 degree rotation about 111) grown from chloride Deposited 2021-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 117-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 21 CL CHLORIDE ION × 42 MG MAGNESIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were equal volumes of 5 mg/ml STMV in 0.1 M phosphate at pH 6.5 and the reservoir solution, which was 8% w/v NaCl in 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.	Resolution 3.20 Å R-free 0.254
7M50 Crystallographic structure of a cubic crystal form of STMV grown from ammonium sulfate Deposited 2021-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 117-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 15 MG MAGNESIUM ION × 15 CL CHLORIDE ION × 3 SO4 SULFATE ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were 6 to 8 ul and were composed of equal volumes of a 5 mg/ml virus stock solution containing 0.1 M phosphate at pH 6.5, and the reservoir solution. The reservoir solution was 18% ammonium sulfate in 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.	Resolution 2.31 Å R-free 0.271
7M54 Crystallographic structure of a cubic crystal form of STMV grown from bromide Deposited 2021-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain C 1–159（159 aa） Chain D 1–159（159 aa） Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain M 1–159（159 aa） Chain N 1–159（159 aa） Chain O 1–159（159 aa）	Not recorded	CA CALCIUM ION × 18 BR BROMIDE ION × 546 MG MAGNESIUM ION × 27 CL CHLORIDE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；279 K；crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1M phosphate, and the reservoir solution. The reservoir solution was 18% w/v NaBr buffered with 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.	Resolution 3.80 Å R-free 0.285
7M57 Crystallographic structure of a primitive orthorhombic crystal form of STMV Deposited 2021-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 218-meric	Chain A 1–159（159 aa） Chain B 1–159（159 aa） Chain BB 1–159（159 aa） Chain C 1–159（159 aa） Chain CC 1–159（159 aa） Chain D 1–159（159 aa） Chain DD 1–159（159 aa） Chain E 1–159（159 aa） Chain EE 1–159（159 aa） Chain F 1–159（159 aa） Chain FF 1–159（159 aa） Chain G 1–159（159 aa） Chain GG 1–159（159 aa） Chain H 1–159（159 aa） Chain HH 1–159（159 aa） Chain I 1–159（159 aa） Chain II 1–159（159 aa） Chain J 1–159（159 aa） Chain JJ 1–159（159 aa） Chain K 1–159（159 aa） Chain KK 1–159（159 aa） Chain L 1–159（159 aa） Chain LL 1–159（159 aa） Chain M 1–159（159 aa） Chain MM 1–159（159 aa） Chain N 1–159（159 aa） Chain NN 1–159（159 aa） Chain O 1–159（159 aa） Chain OO 1–159（159 aa） Chain PP 1–159（159 aa）	Not recorded	PO4 PHOSPHATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH 6.5, and the reservoir. The reservoirs were 16% ammonium sulfate buffered at pH 6.0 with 0.1 M phosphate. Crystallization was a room temperature.	Resolution 4.00 Å

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COAT_STMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159

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	4oq8
Deposition date deposition_date	2014-02-07
Structure title title	Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints
Keywords keywords	Double-helix RNA, Protein-RNA complex, Swiss Jelly-roll beta barrel, VIRUS-RNA complex; VIRUS/RNA
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	21.27 Å
Radius of gyration Rg (electron density) rg_electron	20.75 Å
Forward intensity I(0) i0	13872900.00
Molecular weight molecular_weight	22626.0 kDa
Excluded volume excluded_volume	26041 Å³
Envelope volume envelope_volume	36920 Å³
Hydration-shell volume shell_volume	15873 Å³
Envelope diameter envelope_diameter	79.9 Å
Shell Rg shell_rg	25.92 Å
Envelope Rg envelope_rg	21.94 Å
Shape Rg shape_rg	20.67 Å
Total Rg total_rg	21.62 Å
Total atoms total_atoms	1556
Residues n_residues	164
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	75.9 Å
Rg (real space) rg_real	21.45 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.3870e+07
I(0) uncertainty (real space) i0_real_error	2.0590e+05
Rg (reciprocal space) rg_reciprocal	21.42 Å
I(0) (reciprocal space) i0_reciprocal	13870000.0000
Solution quality estimate total_estimate	0.7473
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.543
Kurtosis Kurtosis kurtosis	-0.075
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2665000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.672; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Coat protein
Molecular weight formula_weight	17533.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1946

MGRGKVKPNRKSTGDNSNVVTMIRAGSYPKVNPTPTWVRAIPFEVSVQSGIAFKVPVGSLFSANFRTDSFTSVTVMSVRAWTQLTPPVNEYSFVRLKPLFKTGDSTEEFEGRASNINTRASVGYRIPTNLRQNTVAADNVCEVRSNCRQVALVISCCFN

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ;
Molecular weight formula_weight	3247.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

AAAAAAAAAA

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	3016.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

UUUUUUUUUU

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(PUPU)-3') ;
Molecular weight formula_weight	567.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

UU

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4oq8a_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.7 — Satellite viruses
Family Family family	b.121.7.1 — Satellite viruses

CATH v4.4 (1 domains)

Domain ID domain_id	4oq8A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

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8. Citations (8)

Satellite tobacco mosaic virus refined to 1.4 angstrom resolution.

Acta Crystallogr.,Sect.D (2014)

PMID: 25195746 · DOI: 10.1107/S1399004714013789 PRIMARY

A model for the structure of satellite tobacco mosaic virus.

J.Struct.Biol. (2012)

PMID: 22750417 · DOI: 10.1016/j.jsb.2012.06.008

Satellite tobacco mosaic virus RNA: structure and implications for assembly.

Curr.Opin.Struct.Biol. (2001)

PMID: 11179893

Refined structure of satellite tobacco mosaic virus at 1.8 A resolution.

J.Mol.Biol. (1998)

PMID: 9514737 · DOI: 10.1006/jmbi.1997.1570

Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution.

J.Mol.Biol. (1993)

PMID: 8510153 · DOI: 10.1006/jmbi.1993.1289

Double-helical RNA in satellite tobacco mosaic virus.

Nature (1993)

PMID: 8421525 · DOI: 10.1038/361179a0

Macromolecular crystal growth experiments on International Microgravity Laboratory--1.

Protein Sci. (1992)

PMID: 1303744 · DOI: 10.1002/pro.5560011004

Preliminary analysis of crystals of satellite tobacco mosaic virus.

J.Mol.Biol. (1989)

PMID: 2585487

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Unit-cell length a length_a	172.690 Å
Unit-cell length b length_b	190.300 Å
Unit-cell length c length_c	201.690 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	120

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	48.350 Å
R factor r_factor	0.2784
R_work r_work	0.2776
R_free r_free	0.2793

fit	/app/data/saxs_computation/oq/4oq8/4oq8.fit
pddf	/app/data/pr_computation/oq/4oq8/4oq8.pr.out
profile	/app/data/saxs_computation/oq/4oq8/4oq8.dat

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints

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

Coat 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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (8)

9. Files and Curves (10)

Files (7)

Curves (3)