ENDONUCLEASE PI-SCEI
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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain A; UniProt 284–466 Chain A; UniProt 693–736 | Fragment:PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE REMARK 999 Mutation:YES | No other associated polymer | X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.8;30 % PEG4000, 0.1 M SODIUM CITRATE PH 5.6, 0.2 M NH4-ACETATE | Resolution 1.35 Å R-free 0.189 |
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 1GPP | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1DFA CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP Deposited 1999-11-18 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
284–737(454 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 8.3;323 K;20% PEG 3350, 100MM TRIS-HCL, 100MM KCL, 200MM MGCL2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 323.0K
|
Resolution 2.00 Å R-free 0.280 |
| 1JVA CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES Deposited 2001-08-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
274–747(474 aa)
Fragment:RESIDUES 274-747
|
Mutation:C284S/H362N/N737S/C738S | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.240 |
| 1JVA CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES Deposited 2001-08-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
274–747(474 aa)
Fragment:RESIDUES 274-747
|
Mutation:C284S/H362N/N737S/C738S | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.240 |
| 1LWS Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence Deposited 2002-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
284–737(454 aa)
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;PEG 200, na hepes, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.50 Å R-free 0.310 |
| 1LWT Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free) Deposited 2002-06-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer;Protein × 1 PDB declaration: trimeric |
Chain A
284–737(454 aa)
|
Non-standard monomer:Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.8;291 K;PEG 3550, na citrate, ammonium acetate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.20 Å R-free 0.287 |
| 1UM2 Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment Deposited 2003-09-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
284–737(454 aa)
Chain C
274–283(10 aa)
Chain C
738–747(10 aa)
|
Mutation:C284S, H362N Mutation:C738S Mutation:C738S | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;PEG 6000, BistrisHCl, 2-mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.90 Å R-free 0.283 |
| 1UM2 Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment Deposited 2003-09-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain B
284–737(454 aa)
Chain D
274–283(10 aa)
Chain D
738–747(10 aa)
|
Mutation:C284S, H362N Mutation:C738S Mutation:C738S | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;PEG 6000, BistrisHCl, 2-mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.90 Å R-free 0.283 |
| 1VDE PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY Deposited 1997-04-01 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
284–737(454 aa)
Chain B
284–737(454 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5;4% PEG 6K, 10MM BME, 3MM CDCL2, 1MM MGCL2, 100MM TRIS, PH=8.5
|
Resolution 2.40 Å R-free 0.238 |
| 3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 28 PDB declaration: 28-meric |
Chain A
2–283(282 aa)
Fragment:SEE REMARK 999
Chain A
738–1071(334 aa)
Fragment:SEE REMARK 999
Chain C
2–283(282 aa)
Fragment:SEE REMARK 999
Chain C
738–1071(334 aa)
Fragment:SEE REMARK 999
Chain E
2–283(282 aa)
Fragment:SEE REMARK 999
Chain E
738–1071(334 aa)
Fragment:SEE REMARK 999
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside;pH 7.4;50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions
Blot for 23 seconds before freezing;77 K;Cryogen OTHER;Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
|
Resolution 6.90 Å |
| 3J9U Yeast V-ATPase state 2 Deposited 2015-02-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 28 PDB declaration: 28-meric |
Chain A
2–283(282 aa)
Fragment:SEE REMARK 999
Chain A
738–1071(334 aa)
Fragment:SEE REMARK 999
Chain C
2–283(282 aa)
Fragment:SEE REMARK 999
Chain C
738–1071(334 aa)
Fragment:SEE REMARK 999
Chain E
2–283(282 aa)
Fragment:SEE REMARK 999
Chain E
738–1071(334 aa)
Fragment:SEE REMARK 999
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside;pH 7.4;50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions
Blot for 23 seconds before freezing;77 K;Cryogen OTHER;Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
|
Resolution 7.60 Å |
| 3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 28 PDB declaration: 28-meric |
Chain A
2–283(282 aa)
Fragment:SEE REMARK 999
Chain A
738–1071(334 aa)
Fragment:SEE REMARK 999
Chain C
2–283(282 aa)
Fragment:SEE REMARK 999
Chain C
738–1071(334 aa)
Fragment:SEE REMARK 999
Chain E
2–283(282 aa)
Fragment:SEE REMARK 999
Chain E
738–1071(334 aa)
Fragment:SEE REMARK 999
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside;pH 7.4;50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions
Blot for 23 seconds before freezing;77 K;Cryogen OTHER;Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
|
Resolution 8.30 Å |
| 5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 14 PDB declaration: tetradecameric |
Chain A
1–283(283 aa)
Chain A
738–1071(334 aa)
Chain B
1–283(283 aa)
Chain B
738–1071(334 aa)
Chain C
1–283(283 aa)
Chain C
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROFLUIDIC;pH 7.5;291 K;9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
|
Resolution 7.00 Å R-free 0.309 |
| 5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 14 PDB declaration: tetradecameric |
Chain a
1–283(283 aa)
Chain a
738–1071(334 aa)
Chain b
1–283(283 aa)
Chain b
738–1071(334 aa)
Chain c
1–283(283 aa)
Chain c
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROFLUIDIC;pH 7.5;291 K;9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
|
Resolution 7.00 Å R-free 0.309 |
| 5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 15 PDB declaration: pentadecameric |
Chain A
1–283(283 aa)
Chain A
738–1071(334 aa)
Chain B
1–283(283 aa)
Chain B
738–1071(334 aa)
Chain C
1–283(283 aa)
Chain C
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
|
Resolution 6.20 Å R-free 0.302 |
| 5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 15 PDB declaration: pentadecameric |
Chain a
1–283(283 aa)
Chain a
738–1071(334 aa)
Chain b
1–283(283 aa)
Chain b
738–1071(334 aa)
Chain c
1–283(283 aa)
Chain c
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
|
Resolution 6.20 Å R-free 0.302 |
| 5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 33 PDB declaration: 33-meric |
Chain A
1–283(283 aa)
Chain A
738–1071(334 aa)
Chain C
1–283(283 aa)
Chain C
738–1071(334 aa)
Chain E
1–283(283 aa)
Chain E
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 6.80 Å |
| 5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 33 PDB declaration: 33-meric |
Chain A
1–283(283 aa)
Chain A
738–1071(334 aa)
Chain C
1–283(283 aa)
Chain C
738–1071(334 aa)
Chain E
1–283(283 aa)
Chain E
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 7.90 Å |
| 5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 33 PDB declaration: 33-meric |
Chain A
1–283(283 aa)
Chain A
738–1071(334 aa)
Chain C
1–283(283 aa)
Chain C
738–1071(334 aa)
Chain E
1–283(283 aa)
Chain E
738–1071(334 aa)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 7.60 Å |
| 9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 14 PDB declaration: 14-meric |
Chain A
1–1071(1071 aa)
Chain E
1–1071(1071 aa)
|
Not recorded | MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | P17255 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 11–193; UniProt 284–466 Author chain A; PDBConstruct 194–237; UniProt 693–736 |