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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P17255 New Search
16PDB entries
20Biological assembly
77chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1DFA CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP Deposited 1999-11-18 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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
1GPP Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I Deposited 2001-11-07 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 284–466（183 aa） Fragment：PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE REMARK 999
Chain A 693–736（44 aa） Fragment：PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE REMARK 999
Mutation：YES Mutation：YES No recorded non-water small molecule 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
1JVA CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES Deposited 2001-08-29 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
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 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric（14） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.