1n9r

Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122

Method: X-RAY DIFFRACTION D_max: 76.2 Å Quality: GOOD

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

Small nuclear ribonucleoprotein F

Saccharomyces cerevisiae

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–86 Chain B； UniProt 1–86 Chain C； UniProt 1–86 Chain D； UniProt 1–86 Chain E； UniProt 1–86 Chain F； UniProt 1–86 Chain G； UniProt 1–86	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K	Resolution 2.80 Å R-free 0.268
2	Protein homooligomer Homooligomer Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain A； UniProt 1–86 Chain B； UniProt 1–86 Chain C； UniProt 1–86 Chain D； UniProt 1–86 Chain E； UniProt 1–86 Chain F； UniProt 1–86 Chain G； UniProt 1–86	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K	Resolution 2.80 Å R-free 0.268

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 1N9R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N9S Crystal structure of yeast SmF in spacegroup P43212 Deposited 2002-11-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–86（86 aa） Chain B 1–86（86 aa） Chain C 1–86（86 aa） Chain D 1–86（86 aa） Chain E 1–86（86 aa） Chain F 1–86（86 aa） Chain G 1–86（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；Tris, PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K	Resolution 3.50 Å R-free 0.297
1N9S Crystal structure of yeast SmF in spacegroup P43212 Deposited 2002-11-26	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 1–86（86 aa） Chain I 1–86（86 aa） Chain J 1–86（86 aa） Chain K 1–86（86 aa） Chain L 1–86（86 aa） Chain M 1–86（86 aa） Chain N 1–86（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；Tris, PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K	Resolution 3.50 Å R-free 0.297
1N9S Crystal structure of yeast SmF in spacegroup P43212 Deposited 2002-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–86（86 aa） Chain B 1–86（86 aa） Chain C 1–86（86 aa） Chain D 1–86（86 aa） Chain E 1–86（86 aa） Chain F 1–86（86 aa） Chain G 1–86（86 aa） Chain H 1–86（86 aa） Chain I 1–86（86 aa） Chain J 1–86（86 aa） Chain K 1–86（86 aa） Chain L 1–86（86 aa） Chain M 1–86（86 aa） Chain N 1–86（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；Tris, PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K	Resolution 3.50 Å R-free 0.297
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric	Chain W 1–86（86 aa） Chain Z 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5GAM Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: Dodecameric	Chain f 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.70 Å
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.70 Å
5GAO Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: 11-meric	Chain q 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 4.20 Å
5GM6 Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution Deposited 2016-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 46-meric	Chain h 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5 ZN ZINC ION × 13 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
5GMK Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution Deposited 2016-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 45-meric	Chain h 1–86（86 aa） Chain w 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8；The CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5LJ3 Structure of the core of the yeast spliceosome immediately after branching Deposited 2016-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 38-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；3 microlitres sample were applied to the grid, left for 30 seconds and then blotted for 2.5-3.0 seconds before plunging.	Resolution 3.80 Å
5LJ5 Overall structure of the yeast spliceosome immediately after branching. Deposited 2016-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 45-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；3 microlitres sample were applied to the grid, left for 30 seconds and then blotted for 2.5-3.0 seconds before plunging.	Resolution 10.00 Å
5LQW yeast activated spliceosome Deposited 2016-08-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 31-meric	Chain f 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
5MPS Structure of a spliceosome remodeled for exon ligation Deposited 2016-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 30-meric	Chain f 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 3 K POTASSIUM ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；NP-40 is also called IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging.	Resolution 3.85 Å
5MQ0 Structure of a spliceosome remodeled for exon ligation Deposited 2016-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 46-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 3 K POTASSIUM ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；NP-40 is also called IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging.	Resolution 4.17 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa） Chain x 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0 cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.	Resolution 7.20 Å
5WSG Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution Deposited 2016-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 45-meric	Chain H 1–86（86 aa） Chain h 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8；10mM Tris-HCl, pH 8.0, 75mM NaCl, 1mM Mg(OAc)2, 1mM imidazole, 0.01% NP40, 1mM TCEP, 0.5mM EGTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
5Y88 Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom Deposited 2017-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 44-meric	Chain c 1–86（86 aa） Chain j 1–86（86 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
5YLZ Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom Deposited 2017-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 43-meric	Chain c 1–86（86 aa） Chain j 1–86（86 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain U 1–86（86 aa） Chain f 1–86（86 aa） Chain j 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5ZWN Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region) Deposited 2018-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain f 1–86（86 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric	Chain U 1–86（86 aa） Chain f 1–86（86 aa） Chain j 1–86（86 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6BK8 S. cerevisiae spliceosomal post-catalytic P complex Deposited 2017-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 46-meric	Chain b 1–86（86 aa） Chain m 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 5 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6EXN Post-catalytic P complex spliceosome with 3' splice site docked Deposited 2017-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 40-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；3 uL sample was applied to the grid, left for 30s, then blotted for 3s and immediately plunged into liquid ethane.	Resolution 3.70 Å
6G90 Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2) Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 38-meric	Chain f 1–86（86 aa） Chain x 1–86（86 aa）	Not recorded	ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2-3.5 s and vitrified by plunging into liquid ethane with a FEI Vitrobot Mark III operated at 4 degree Celsius and 100% humidity.	Resolution 4.00 Å
6J6G Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom Deposited 2019-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 41-meric	Chain h 1–86（86 aa） Chain w 1–86（86 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6J6H Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom Deposited 2019-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 41-meric	Chain h 1–86（86 aa） Chain w 1–86（86 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6J6N Cryo-EM structure of the yeast B*-b1 complex at an average resolution of 3.86 angstrom Deposited 2019-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 41-meric	Chain h 1–86（86 aa） Chain w 1–86（86 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.86 Å
6J6Q Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom Deposited 2019-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 42-meric	Chain h 1–86（86 aa） Chain w 1–86（86 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6N7P S. cerevisiae spliceosomal E complex (UBC4) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain P 1–86（86 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6N7R Saccharomyces cerevisiae spliceosomal E complex (ACT1) Deposited 2018-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain P 1–86（86 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6N7X S. cerevisiae U1 snRNP Deposited 2018-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain P 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7B9V Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound Deposited 2020-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 50-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 6 K POTASSIUM ION × 1 KGN D-chiro inositol hexakisphosphate × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7OQB The U2 part of Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1) Deposited 2021-06-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain x 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
7OQC The U1 part of Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1) Deposited 2021-06-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain f 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7OQE Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1) Deposited 2021-06-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 39-meric	Chain f 1–86（86 aa） Chain x 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
8W2O Yeast U1 snRNP with humanized U1C Zinc-Finger domain Deposited 2024-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: 18-meric	Chain P 1–86（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM Hepes, pH7.9, 120 mM KCl, 2 mM EGTA cryo-EM vitrification conditions Cryogen ETHANE；The grids were obtained with the chamber at 100% humidity, 2.5 s blotting time, -6 blotting force and 15 s wait time and flash-frozen into liquid ethane with a Vitrobot Mark IV (Thermo Fisher Scientific)	Resolution 3.49 Å
9DTR Structure of the yeast post-catalytic P complex spliceosome at 2.3 Angstrom resolution Deposited 2024-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 47-meric	Chain f 1–86（86 aa） Chain q 1–86（86 aa）	Not recorded	MG MAGNESIUM ION × 2 K POTASSIUM ION × 4 IHP INOSITOL HEXAKISPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.31 Å

35 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RUXF_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–93； UniProt 1–86 Author chain B； PDBConstruct 8–93； UniProt 1–86 Author chain C； PDBConstruct 8–93； UniProt 1–86 Author chain D； PDBConstruct 8–93； UniProt 1–86 Author chain E； PDBConstruct 8–93； UniProt 1–86 Author chain F； PDBConstruct 8–93； UniProt 1–86 Author chain G； PDBConstruct 8–93； UniProt 1–86

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	1n9r
Deposition date deposition_date	2002-11-26
Structure title title	Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122
Keywords keywords	snrnp, Sm protein, heptamer, TRANSLATION; TRANSLATION
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	25.59 Å
Radius of gyration Rg (electron density) rg_electron	24.20 Å
Forward intensity I(0) i0	47511200.00
Molecular weight molecular_weight	54284.0 kDa
Excluded volume excluded_volume	68243 Å³
Envelope volume envelope_volume	83053 Å³
Hydration-shell volume shell_volume	27948 Å³
Envelope diameter envelope_diameter	75.5 Å
Shell Rg shell_rg	31.72 Å
Envelope Rg envelope_rg	23.90 Å
Shape Rg shape_rg	24.21 Å
Total Rg total_rg	25.02 Å
Total atoms total_atoms	3837
Residues n_residues	478
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	76.2 Å
Rg (real space) rg_real	25.46 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	4.7510e+07
I(0) uncertainty (real space) i0_real_error	6.9290e+05
Rg (reciprocal space) rg_reciprocal	25.50 Å
I(0) (reciprocal space) i0_reciprocal	47510000.0000
Solution quality estimate total_estimate	0.8978
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.096
Kurtosis Kurtosis kurtosis	-0.700
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47050000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.779

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1n9ra_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1n9rb_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1n9rc_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1n9rd_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1n9re_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1n9rf_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d1n9rg_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

CATH v4.4 (7 domains)

Domain ID domain_id	1n9rA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1n9rB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1n9rC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1n9rD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1n9rE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1n9rF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1n9rG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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8. Citations (1)

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Unit-cell length a length_a	79.891 Å
Unit-cell length b length_b	79.891 Å
Unit-cell length c length_c	251.188 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	56

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2543
R_work r_work	0.2536
R_free r_free	0.2678

Description description	Small nuclear ribonucleoprotein F
Molecular weight formula_weight	10630.0 kDa
Source method src_method	man
Copy count entity_count	7

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	3837

Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122

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

Small nuclear ribonucleoprotein F

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/n9/1n9r/1n9r.fit
pddf	/app/data/pr_computation/n9/1n9r/1n9r.pr.out
profile	/app/data/saxs_computation/n9/1n9r/1n9r.dat