SAXSdb — 8yas

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

Protein translocase subunit SecA

Bacillus subtilis subsp. subtilis str. 168

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–778	Not recorded	Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.97 Å

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 8YAS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M6N Crystal structure of the SecA translocation ATPase from Bacillus subtilis Deposited 2002-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–802（802 aa）	Not recorded	SO4 SULFATE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；2 M ammonium sulfate, 30% glycerol, 1 mM DTT, 100 mM BES, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 299K	Resolution 2.70 Å R-free 0.301
1M74 Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis Deposited 2002-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–802（802 aa）	Not recorded	MG MAGNESIUM ION × 2 SO4 SULFATE ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；5 mM ADP, 5 mM MgCl, 2 M ammonium sulfate, 30% glycerol, 1 mM DTT, 100 mM BES, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 299K	Resolution 3.00 Å R-free 0.291
1TF2 Crystal structure of SecA:ADP in an open conformation from Bacillus Subtilis Deposited 2004-05-26	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 1–841（841 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 250mM Magnesium Acetate, 7-12% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.292
1TF5 Crystal structure of SecA in an open conformation from Bacillus Subtilis Deposited 2004-05-26	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 1–841（841 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 250mM Magnesium Acetate, 7-12% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.18 Å R-free 0.273
2IBM A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA Deposited 2006-09-11	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 1–780（780 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；301 K；1.8 M malonate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 301K	Resolution 3.20 Å R-free 0.323
2IBM A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA Deposited 2006-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–780（780 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；301 K；1.8 M malonate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 301K	Resolution 3.20 Å R-free 0.323
2IBM A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–780（780 aa） Chain B 1–780（780 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；301 K；1.8 M malonate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 301K	Resolution 3.20 Å R-free 0.323
2IBM A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–780（780 aa） Chain B 1–780（780 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；301 K；1.8 M malonate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 301K	Resolution 3.20 Å R-free 0.323
3DL8 Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA Deposited 2008-06-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–779（779 aa） Fragment：UNP residues 1-779	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；26-28% (w/v) PEG 3350 and 250mM lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 7.50 Å R-free 0.390
3DL8 Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA Deposited 2008-06-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–779（779 aa） Fragment：UNP residues 1-779	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；26-28% (w/v) PEG 3350 and 250mM lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 7.50 Å R-free 0.390
3IQM Active site mutants of B. subtilis SecA Deposited 2009-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–802（802 aa） Fragment：UNP residues 1-802	Mutation：E208Q	SO4 SULFATE ION × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；20 mM BES pH 7.0, 2.12 M Ammonium sulfate, 31% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 3.40 Å R-free 0.267
3IQY Active site mutants of B. subtilis SecA Deposited 2009-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–841（841 aa）	Mutation：E208Q, R489K	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；20 mM BES pH 7.0, 2.1 M Ammonium sulfate, 32 % Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 3.30 Å R-free 0.269
5EUL Structure of the SecA-SecY complex with a translocating polypeptide substrate Deposited 2015-11-18	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 × 4 PDB declaration: tetrameric	Chain A 1–742（742 aa） Chain A 744–780（37 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 TBR HEXATANTALUM DODECABROMIDE × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；21-24% polyethylene glycol 1500, 100mM Tris-HCl pH8.5, 50-100 mM MgAc2, 2% 2-methyl-2,4-pentandiol	Resolution 3.70 Å R-free 0.315
6ITC Structure of a substrate engaged SecA-SecY protein translocation machine Deposited 2018-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–780（780 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
7XHA Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-. Deposited 2022-04-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–778（778 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
7XHB Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP Deposited 2022-04-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–778（778 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
8Y9Y Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C) Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–778（778 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8Y9Z Structure of the SecA-SecY complex with the substrate HmBRI-3TM Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–778（778 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
8YA0 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) Deposited 2024-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 14–778（765 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
8YA2 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C) Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–778（778 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SECA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–778； UniProt 1–778

Protein translocase subunit SecY

Geobacillus thermodenitrificans NG80-2

UniProt A4IJK8

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Y； UniProt 1–430	Mutation：G60C, Q202T, F211T, R213N	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecE × 1 （A4IJH4） MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.97 Å

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 8YAS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EUL Structure of the SecA-SecY complex with a translocating polypeptide substrate Deposited 2015-11-18	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 × 4 PDB declaration: tetrameric	Chain Y 1–430（430 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 TBR HEXATANTALUM DODECABROMIDE × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；21-24% polyethylene glycol 1500, 100mM Tris-HCl pH8.5, 50-100 mM MgAc2, 2% 2-methyl-2,4-pentandiol	Resolution 3.70 Å R-free 0.315
6ITC Structure of a substrate engaged SecA-SecY protein translocation machine Deposited 2018-11-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain Y 1–430（430 aa）	Mutation：G60C,Q202T,L210G,F211G,R213N	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
7XHA Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-. Deposited 2022-04-07	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Y 1–430（430 aa）	Mutation：G60C	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
7XHB Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP Deposited 2022-04-07	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Y 1–430（430 aa）	Mutation：G60C	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
8Y9Y Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C) Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Y 1–430（430 aa）	Mutation：G60C, Q202T, F211T, R213N	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8Y9Z Structure of the SecA-SecY complex with the substrate HmBRI-3TM Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain Y 1–430（430 aa）	Mutation：G60C, Q202T, F211T, R213N	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
8YA0 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) Deposited 2024-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain Y 2–430（429 aa）	Mutation：G60C, Q202T, F211T, R213N	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
8YA2 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C) Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain Y 1–430（430 aa）	Mutation：G60C, Q202T, F211T, R213N	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YA3 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT Deposited 2024-02-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 1–430（430 aa）	Mutation：G60C, Q202T, F211T, R213N	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A4IJK8_GEOTN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Y； PDBConstruct 1–430； UniProt 1–430

Protein translocase subunit SecE

Geobacillus thermodenitrificans NG80-2

UniProt A4IJH4

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 1–60	Not recorded	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.97 Å

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 8YAS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EUL Structure of the SecA-SecY complex with a translocating polypeptide substrate Deposited 2015-11-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 TBR HEXATANTALUM DODECABROMIDE × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；21-24% polyethylene glycol 1500, 100mM Tris-HCl pH8.5, 50-100 mM MgAc2, 2% 2-methyl-2,4-pentandiol	Resolution 3.70 Å R-free 0.315
6ITC Structure of a substrate engaged SecA-SecY protein translocation machine Deposited 2018-11-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
7XHA Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-. Deposited 2022-04-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
7XHB Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP Deposited 2022-04-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
8Y9Y Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C) Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8Y9Z Structure of the SecA-SecY complex with the substrate HmBRI-3TM Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
8YA0 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) Deposited 2024-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 2–59（58 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
8YA2 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C) Deposited 2024-02-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–60（60 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YA3 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT Deposited 2024-02-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–60（60 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A4IJH4_GEOTN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–60； UniProt 1–60

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8yas
Deposition date deposition_date	2024-02-10
Structure title title	Structure of the SecA-SecY complex with the substrate HmBRI-7TM
Keywords keywords	Protein translocation, SecY, Membrane protein insertion, Protein chaperone, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.91 Å
Radius of gyration Rg (electron density) rg_electron	36.57 Å
Forward intensity I(0) i0	286372000.00
Molecular weight molecular_weight	140630.0 kDa
Excluded volume excluded_volume	177820 Å³
Envelope volume envelope_volume	236550 Å³
Hydration-shell volume shell_volume	53613 Å³
Envelope diameter envelope_diameter	121.8 Å
Shell Rg shell_rg	43.03 Å
Envelope Rg envelope_rg	36.04 Å
Shape Rg shape_rg	36.57 Å
Total Rg total_rg	36.98 Å
Total atoms total_atoms	9894
Residues n_residues	1243
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	113.2 Å
Rg (real space) rg_real	36.78 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	2.8640e+08
I(0) uncertainty (real space) i0_real_error	4.4270e+06
Rg (reciprocal space) rg_reciprocal	36.86 Å
I(0) (reciprocal space) i0_reciprocal	286400000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.1 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.598
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41380000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.815

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Protein translocase subunit SecA
Molecular weight formula_weight	88673.9 kDa
EC 编号 ec_number	7.4.2.8
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	9894

MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA

来源 Source

来源生物 organism	Bacillus subtilis subsp. subtilis str. 168
NCBI Class编号 ncbi_taxonomy_id	224308
宿主生物 host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Protein translocase subunit SecY
Molecular weight formula_weight	47512.1 kDa
Mutation mutation	G60C, Q202T, F211T, R213N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCGGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLGFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISIIIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYRGFIK

来源 Source

来源生物 organism	Geobacillus thermodenitrificans NG80-2
NCBI Class编号 ncbi_taxonomy_id	420246
宿主生物 host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	Protein translocase subunit SecE
Molecular weight formula_weight	8249.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFEGGHHHHHHHH

来源 Source

来源生物 organism	Geobacillus thermodenitrificans NG80-2
NCBI Class编号 ncbi_taxonomy_id	420246
宿主生物 host_organism	Escherichia coli K-12

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.97 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	148826

fit	/app/data/saxs_computation/ya/8yas/8yas.fit
pddf	/app/data/pr_computation/ya/8yas/8yas.pr.out
profile	/app/data/saxs_computation/ya/8yas/8yas.dat

Structure of the SecA-SecY complex with the substrate HmBRI-7TM

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

Protein translocase subunit SecA

State in the Current Structure

Other States of the Same Protein in the Database

Protein translocase subunit SecY

State in the Current Structure

Other States of the Same Protein in the Database

Protein translocase subunit SecE

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)