Pescadillo homolog 1
Homo sapiens
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 322–414 | Fragment:BRCT domain | No other associated polymer | SOLUTION NMR NMR measurement conditions:pH 7;293 K;Ionic strength (raw mmCIF value) 120mM;Pressure ambient NMR sample composition:0.46mM uniformly 13C,15N-labeled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3; 10% D2O, 90% H2O | 10% D2O, 90% H2O | Resolution not provided |
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 2EP8 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 8FKP Human nucleolar pre-60S ribosomal subunit (State A1) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 44 PDB declaration: 47-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 54 ZN ZINC ION × 2 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the Vitrobot.
|
Resolution 2.85 Å |
| 8FKQ Human nucleolar pre-60S ribosomal subunit (State A2) Deposited 2022-12-21 | Different construct 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: 43-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 51 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.76 Å |
| 8FKR Human nucleolar pre-60S ribosomal subunit (State B1) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 48 PDB declaration: 51-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 54 ZN ZINC ION × 2 SF4 IRON/SULFUR CLUSTER × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.89 Å |
| 8FKS Human nucleolar pre-60S ribosomal subunit (State B2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 44 PDB declaration: 47-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 61 ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.88 Å |
| 8FKT Human nucleolar pre-60S ribosomal subunit (State C1) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 50 PDB declaration: 53-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 64 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.81 Å |
| 8FKU Human nucleolar pre-60S ribosomal subunit (State C2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 47 PDB declaration: 50-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 58 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.82 Å |
| 8FKV Human nucleolar pre-60S ribosomal subunit (State D1) Deposited 2022-12-21 | Different construct 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: 56-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 65 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.47 Å |
| 8FKW Human nucleolar pre-60S ribosomal subunit (State D2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 50 PDB declaration: 53-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 59 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.50 Å |
| 8FKX Human nucleolar pre-60S ribosomal subunit (State E) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 50 PDB declaration: 53-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 61 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.59 Å |
| 8FKY Human nucleolar pre-60S ribosomal subunit (State F) Deposited 2022-12-21 | Different construct 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 SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 70 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.67 Å |
| 8FKZ Human nucleolar pre-60S ribosomal subunit (State G) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 48 PDB declaration: 51-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 64 ZN ZINC ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 3.04 Å |
| 8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21 | 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: 65-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.67 Å |
| 8FL3 Human nuclear pre-60S ribosomal subunit (State I2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 60 PDB declaration: 63-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.53 Å |
| 8FL4 Human nuclear pre-60S ribosomal subunit (State I3) Deposited 2022-12-21 | Different construct 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 SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 99 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.89 Å |
| 8FL6 Human nuclear pre-60S ribosomal subunit (State J1) Deposited 2022-12-21 | 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: 56-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.62 Å |
| 8FL7 Human nuclear pre-60S ribosomal subunit (State J2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 51 PDB declaration: 54-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.55 Å |
| 8FLA Human nuclear pre-60S ribosomal subunit (State K1) Deposited 2022-12-21 | 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: 56-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.63 Å |
| 8FLB Human nuclear pre-60S ribosomal subunit (State K2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 51 PDB declaration: 54-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the vitrobot.
|
Resolution 2.55 Å |
| 8FLD Human nuclear pre-60S ribosomal subunit (State L1) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 50 PDB declaration: 54-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 87 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the Vitrobot.
|
Resolution 2.58 Å |
| 8FLE Human nuclear pre-60S ribosomal subunit (State L2) Deposited 2022-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 49 PDB declaration: 52-meric |
Chain SM
1–588(588 aa)
|
Not recorded | MG MAGNESIUM ION × 87 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE;Four applications with manual blotting before last blotting with the Vitrobot.
|
Resolution 2.48 Å |
| 8INE human nuclear pre-60S ribosomal particle - State G' Deposited 2023-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 54 PDB declaration: 58-meric |
Chain v
1–588(588 aa)
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8INF human nuclear pre-60S ribosomal particle - State F' Deposited 2023-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 57 PDB declaration: 61-meric |
Chain v
1–588(588 aa)
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8IPX human nuclear pre-60S ribosomal particle - State C' Deposited 2023-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 54 PDB declaration: 58-meric |
Chain q
1–588(588 aa)
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 8IPY human nuclear pre-60S ribosomal particle - State D' Deposited 2023-03-15 | 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: 59-meric |
Chain q
1–588(588 aa)
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8IR3 human nuclear pre-60S ribosomal particle - State B' Deposited 2023-03-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 55 PDB declaration: 59-meric |
Chain q
1–588(588 aa)
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PESC_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 8–100; UniProt 322–414 |