4nut

Crystal structure of the complex between Snu13p and the PEP domain of Rsa1

Method: X-RAY DIFFRACTION D_max: 55.6 Å Quality: GOOD

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

13 kDa ribonucleoprotein-associated protein

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–126	Not recorded	Ribosome assembly 1 protein × 1 （Q08932） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.3M ammonium sulfate, 70mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.55 Å R-free 0.235

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 4NUT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZWZ Structural comparison of Yeast snoRNP and splicesomal protein snu13p with its homologs Deposited 2005-06-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.209
1ZWZ Structural comparison of Yeast snoRNP and splicesomal protein snu13p with its homologs Deposited 2005-06-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–126（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.209
2ALE Crystal structure of yeast RNA splicing factor Snu13p Deposited 2005-08-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate, 30% PEG 8K, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.248
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23	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 M 1–126（126 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
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15	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 K 1–126（126 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.70 Å
5GAP Body region of the U4/U6.U5 tri-snRNP Deposited 2015-12-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: Dodecameric	Chain K 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted at 4 deg C for 2 seconds before plunging.	Resolution 3.60 Å
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24	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 K 1–126（126 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
5TZS Architecture of the yeast small subunit processome Deposited 2016-11-22	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 × 52 PDB declaration: 58-meric	Chain e 1–126（126 aa） Chain f 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE；Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing.	Resolution 5.10 Å
5WLC The complete structure of the small subunit processome Deposited 2017-07-26	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 Heteromer；Protein × 67 PDB declaration: 70-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5WYJ Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1) Deposited 2017-01-13	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 × 61 PDB declaration: 64-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.70 Å
5WYK Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP) Deposited 2017-01-13	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: 58-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging	Resolution 4.50 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 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 M 1–126（126 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
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16	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 M 1–126（126 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
6KE6 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome Deposited 2019-07-03	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 × 68 PDB declaration: 71-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；wait 30s and blot 2s before plunging	Resolution 3.40 Å
6LQP Cryo-EM structure of 90S small subunit preribosomes in transition states (State A) Deposited 2020-01-14	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 × 70 PDB declaration: 73-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6LQQ Cryo-EM structure of 90S small subunit preribosomes in transition states (State B) Deposited 2020-01-14	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 × 67 PDB declaration: 70-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6LQR Cryo-EM structure of 90S small subunit preribosomes in transition states (State C) Deposited 2020-01-14	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 × 65 PDB declaration: 68-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.60 Å
6LQS Cryo-EM structure of 90S small subunit preribosomes in transition states (State D) Deposited 2020-01-14	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 × 76 PDB declaration: 79-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6LQT Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) Deposited 2020-01-14	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 × 55 PDB declaration: 58-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
6LQU Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1) Deposited 2020-01-14	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 × 69 PDB declaration: 72-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6LQV Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1) Deposited 2020-01-14	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 × 55 PDB declaration: 58-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6ND4 Conformational switches control early maturation of the eukaryotic small ribosomal subunit Deposited 2018-12-13	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 × 27 PDB declaration: 30-meric	Chain e 1–126（126 aa） Chain f 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
6ZQA Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) Deposited 2020-07-09	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 × 57 PDB declaration: 60-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6ZQB Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state B2 Deposited 2020-07-09	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 × 68 PDB declaration: 71-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6ZQC Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Pre-A1 Deposited 2020-07-09	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 × 68 PDB declaration: 71-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6ZQD Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1 Deposited 2020-07-09	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 × 63 PDB declaration: 66-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6ZQE Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-A (Poly-Ala) Deposited 2020-07-09	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 × 59 PDB declaration: 62-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
7AJT Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome) Deposited 2020-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7AJU Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome) Deposited 2020-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7D4I Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F) Deposited 2020-09-24	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 × 79 PDB declaration: 82-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7D5S Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2) Deposited 2020-09-28	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 × 55 PDB declaration: 58-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7D5T Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) Deposited 2020-09-28	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 × 52 PDB declaration: 55-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.00 Å
7D63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C) Deposited 2020-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain 3G 1–126（126 aa） Chain 3H 1–126（126 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.30 Å
9G33 Stalled 90S - Utp23-Krr1-deltaC3 Deposited 2024-07-11	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 × 62 PDB declaration: 65-meric	Chain CF 1–126（126 aa） Chain CG 1–126（126 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9N6V SSU processome maturation and disassembly, State A Deposited 2025-02-05	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 × 69 PDB declaration: 72-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 25 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9N6W SSU processome maturation and disassembly, State A* Deposited 2025-02-05	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 × 69 PDB declaration: 72-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 25 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9N6X SSU processome maturation and disassembly, State B Deposited 2025-02-05	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 × 69 PDB declaration: 72-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 34 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
9N6Y SSU processome maturation and disassembly, State C Deposited 2025-02-05	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 × 70 PDB declaration: 73-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 34 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9N6Z SSU processome maturation and disassembly, State D Deposited 2025-02-05	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 × 69 PDB declaration: 72-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.74 Å
9N70 SSU processome maturation and disassembly, State E Deposited 2025-02-05	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 × 69 PDB declaration: 72-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.17 Å
9N72 SSU processome maturation and disassembly, State F Deposited 2025-02-05	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 × 70 PDB declaration: 73-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.94 Å
9N73 SSU processome maturation and disassembly, State G Deposited 2025-02-05	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 × 71 PDB declaration: 74-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.96 Å
9N74 SSU processome maturation and disassembly, State H Deposited 2025-02-05	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 × 68 PDB declaration: 71-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 39 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å
9N75 SSU processome maturation and disassembly, State I Deposited 2025-02-05	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 × 65 PDB declaration: 68-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 59 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9N76 SSU processome maturation and disassembly, State J Deposited 2025-02-05	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 × 64 PDB declaration: 67-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 38 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9N77 SSU processome maturation and disassembly, State K Deposited 2025-02-05	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 × 61 PDB declaration: 64-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 48 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9N78 SSU processome maturation and disassembly, State L Deposited 2025-02-05	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 × 56 PDB declaration: 59-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.17 Å
9N79 SSU processome maturation and disassembly, State M Deposited 2025-02-05	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: 45-meric	Chain SE 1–126（126 aa） Chain SF 1–126（126 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å

47 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNU13_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–129； UniProt 1–126

Ribosome assembly 1 protein

Saccharomyces cerevisiae

UniProt Q08932

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 238–290	Fragment：PEP domain, UNP residues 238-290	13 kDa ribonucleoprotein-associated protein × 1 （P39990） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.3M ammonium sulfate, 70mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.55 Å R-free 0.235

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4NUT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M3F NMR structure of Rsa1p238-259 from S. Cerevisiae Deposited 2013-01-17	Different construct 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 238–259（22 aa） Fragment：UNP residues 238-259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.7；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR measurement conditions pH 3.7；305 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 2 mM protein, 10 mM potassium phosphate, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MJF Solution structure of the complex between the yeast Rsa1 and Hit1 proteins Deposited 2014-01-08	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 317–352（36 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] rsa, 1 mM [U-100% 13C; U-100% 15N] hit, 150 mM sodium chloride, 90 % H2O, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RSA1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–57； UniProt 238–290

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	4nut
Deposition date deposition_date	2013-12-04
Structure title title	Crystal structure of the complex between Snu13p and the PEP domain of Rsa1
Keywords keywords	SnoRNP assembly, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	15.96 Å
Radius of gyration Rg (electron density) rg_electron	14.46 Å
Forward intensity I(0) i0	5252310.00
Molecular weight molecular_weight	16733.0 kDa
Excluded volume excluded_volume	21173 Å³
Envelope volume envelope_volume	23428 Å³
Hydration-shell volume shell_volume	13565 Å³
Envelope diameter envelope_diameter	53.2 Å
Shell Rg shell_rg	20.51 Å
Envelope Rg envelope_rg	14.87 Å
Shape Rg shape_rg	14.43 Å
Total Rg total_rg	15.74 Å
Total atoms total_atoms	1172
Residues n_residues	149
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	55.6 Å
Rg (real space) rg_real	15.85 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	5.2520e+06
I(0) uncertainty (real space) i0_real_error	5.3090e+04
Rg (reciprocal space) rg_reciprocal	15.87 Å
I(0) (reciprocal space) i0_reciprocal	5252000.0000
Solution quality estimate total_estimate	0.8428
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.143
Kurtosis Kurtosis kurtosis	-0.260
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1384000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.999

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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	13 kDa ribonucleoprotein-associated protein
Molecular weight formula_weight	13875.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1267

GPHMSAPNPKAFPLADAALTQQILDVVQQAANLRQLKKGANEATKTLNRGISEFIIMAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQIYAVKDKIETLLI

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribosome assembly 1 protein
Molecular weight formula_weight	7015.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPHMTDEDVKKWREERKKMWLLKISNNKQKHMQEMGIKEDELKSQPSIFKESRKEKQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4nutA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

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8. Citations (1)

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Unit-cell length a length_a	59.732 Å
Unit-cell length b length_b	59.732 Å
Unit-cell length c length_c	92.549 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	36.580 Å
R factor r_factor	0.1983
R_work r_work	0.1965
R_free r_free	0.2351

fit	/app/data/saxs_computation/nu/4nut/4nut.fit
pddf	/app/data/pr_computation/nu/4nut/4nut.pr.out
profile	/app/data/saxs_computation/nu/4nut/4nut.dat

Crystal structure of the complex between Snu13p and the PEP domain of Rsa1

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

13 kDa ribonucleoprotein-associated protein

State in the Current Structure

Other States of the Same Protein in the Database

Ribosome assembly 1 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 (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 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)