rRNA biogenesis protein RRP5
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain A; UniProt 1399–1729 | Fragment:UNP residues 1399-1729 | SO4 SULFATE ION × 3 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, pH 5.6 | Resolution 2.81 Å R-free 0.258 |
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 5WWM | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 5C9S Crystal Structure of the C-terminal domain of Rrp5 Deposited 2015-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1163–1729(567 aa)
Fragment:unp residues 1163-1729
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammuniom tartrate, 20% PEG3350
|
Resolution 2.70 Å R-free 0.283 |
| 5NLG RRP5 C-terminal domain Deposited 2017-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1408–1721(314 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;292 K;16-21% PEG1000
100mM Sodium/potassium phosphate, pH 6.0
|
Resolution 2.35 Å R-free 0.241 |
| 5WLC The complete structure of the small subunit processome Deposited 2017-07-26 | Different construct 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 NJ
1–1729(1729 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 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 R2
1–1729(1729 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 |
| 6LQQ Cryo-EM structure of 90S small subunit preribosomes in transition states (State B) Deposited 2020-01-14 | Different construct 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 |
| 6ZQC Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Pre-A1 Deposited 2020-07-09 | Different construct 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 JI
1–1729(1729 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 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 JI
1–1729(1729 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 |
| 7AJT Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome) Deposited 2020-09-29 | Different construct 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 JI
1–1729(1729 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 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 JI
1–1729(1729 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 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 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 RD
1–1729(1729 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 |
| 7SUK Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells Deposited 2021-11-17 | Different construct 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 NJ
1457–1721(265 aa)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.99 Å |
| 9N6V SSU processome maturation and disassembly, State A Deposited 2025-02-05 | Different construct 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 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 OA
1–1729(1729 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 |
27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RRP5_YEAST |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–331; UniProt 1399–1729 |