SAXSdb — 5mg3

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

Protein translocase subunit SecY

Escherichia coli

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain Y； UniProt 1–443	Not recorded	Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 14.00 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 5MG3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J45 Structure of a non-translocating SecY protein channel with the 70S ribosome Deposited 2013-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: undecameric	Chain y 6–440（435 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM HEPES-KOH, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM；pH 7.5；50 mM HEPES-KOH, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM cryo-EM vitrification conditions 90 K；Cryogen ETHANE；Blot 1 second before plunging into liquid ethane (HOMEMADE PLUNGER).	Resolution 9.50 Å
3J46 Structure of the SecY protein translocation channel in action Deposited 2013-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: tetradecameric	Chain y 6–440（435 aa）	Mutation：S68C Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM；pH 7.2；50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM cryo-EM vitrification conditions 77 K；Cryogen ETHANE；Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).	Resolution 10.10 Å
5GAE RNC in complex with a translocating SecYEG Deposited 2015-11-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 36-meric	Chain g 1–443（443 aa）	Not recorded	MG MAGNESIUM ION × 323 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
5NCO Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome Deposited 2017-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 40-meric	Chain g 14–429（416 aa）	Not recorded	ZN ZINC ION × 1 ALF TETRAFLUOROALUMINATE ION × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6R7L Ribosome-bound SecYEG translocon in a nanodisc Deposited 2019-03-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 1–443（443 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.00 Å
9RBF Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC Deposited 2025-05-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric	Chain 6 1–443（443 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.44 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SECY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Y； PDBConstruct 16–458； UniProt 1–443

Protein translocase subunit SecE

Escherichia coli

UniProt P0AG96

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 3–127	Not recorded	Protein translocase subunit SecY × 1 （P0AGA2） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 14.00 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 5MG3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J45 Structure of a non-translocating SecY protein channel with the 70S ribosome Deposited 2013-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: undecameric	Chain E 74–127（54 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM HEPES-KOH, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM；pH 7.5；50 mM HEPES-KOH, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM cryo-EM vitrification conditions 90 K；Cryogen ETHANE；Blot 1 second before plunging into liquid ethane (HOMEMADE PLUNGER).	Resolution 9.50 Å
3J46 Structure of the SecY protein translocation channel in action Deposited 2013-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: tetradecameric	Chain E 74–127（54 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM；pH 7.2；50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM cryo-EM vitrification conditions 77 K；Cryogen ETHANE；Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).	Resolution 10.10 Å
5GAE RNC in complex with a translocating SecYEG Deposited 2015-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 36-meric	Chain h 1–127（127 aa）	Not recorded	MG MAGNESIUM ION × 323 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
5NCO Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome Deposited 2017-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 40-meric	Chain h 67–122（56 aa）	Not recorded	ZN ZINC ION × 1 ALF TETRAFLUOROALUMINATE ION × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
9RBF Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC Deposited 2025-05-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric	Chain 7 1–127（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.44 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SECE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 16–140； UniProt 3–127

Protein-export membrane protein SecG

Escherichia coli

UniProt P0AG99

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 1–110	Not recorded	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 14.00 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 5MG3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J45 Structure of a non-translocating SecY protein channel with the 70S ribosome Deposited 2013-06-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: undecameric	Chain G 9–73（65 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM HEPES-KOH, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM；pH 7.5；50 mM HEPES-KOH, 100 mM KOAc, 10 mM Mg(OAc)2, 0.05% DDM cryo-EM vitrification conditions 90 K；Cryogen ETHANE；Blot 1 second before plunging into liquid ethane (HOMEMADE PLUNGER).	Resolution 9.50 Å
3J46 Structure of the SecY protein translocation channel in action Deposited 2013-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: tetradecameric	Chain G 9–73（65 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM；pH 7.2；50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM cryo-EM vitrification conditions 77 K；Cryogen ETHANE；Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).	Resolution 10.10 Å
5NCO Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome Deposited 2017-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 40-meric	Chain j 1–71（71 aa）	Not recorded	ZN ZINC ION × 1 ALF TETRAFLUOROALUMINATE ION × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
9RBF Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC Deposited 2025-05-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric	Chain 8 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.44 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SECG_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 27–136； UniProt 1–110

Protein translocase subunit SecD

Escherichia coli

UniProt P0AG90

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 2–615	Not recorded	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 14.00 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SECD_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 9–622； UniProt 2–615

Protein translocase subunit SecF

Escherichia coli

UniProt P0AG93

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 1–323	Not recorded	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Membrane protein insertase YidC × 1 （P25714）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 14.00 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SECF_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–323； UniProt 1–323

Membrane protein insertase YidC

Escherichia coli

UniProt P25714

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 2–548	Not recorded	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 14.00 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 5MG3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–340（315 aa） Fragment：UNP residues 26-340	Mutation：E228A, K229A, E231A, K232A, K234A 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 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.249
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–340（315 aa） Fragment：UNP residues 26-340	Mutation：E228A, K229A, E231A, K232A, K234A 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 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.249
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 26–340（315 aa） Fragment：UNP residues 26-340 Chain B 26–340（315 aa） Fragment：UNP residues 26-340	Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E228A, K229A, E231A, K232A, K234A 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 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.249
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22	Different construct Different mutation/modification 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 56–329（274 aa） Fragment：UNP residues 56-329	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 5 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K	Resolution 1.80 Å R-free 0.213
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22	Different construct Different mutation/modification 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 56–329（274 aa） Fragment：UNP residues 56-329	Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 4 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K	Resolution 1.80 Å R-free 0.213
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22	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 56–329（274 aa） Fragment：UNP residues 56-329 Chain B 56–329（274 aa） Fragment：UNP residues 56-329	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 10 PG4 TETRAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 6 EDO 1,2-ETHANEDIOL × 14 2PE NONAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K	Resolution 1.80 Å R-free 0.213
4UTQ A structural model of the active ribosome-bound membrane protein insertase YidC Deposited 2014-07-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–548（548 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,	Resolution 8.00 Å
9RBF Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC Deposited 2025-05-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric	Chain 9 1–548（548 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.44 Å

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YIDC_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 7–553； UniProt 2–548

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	5mg3
Deposition date deposition_date	2016-11-20
Structure title title	EM fitted model of bacterial holo-translocon
Keywords keywords	holotranslocon, membrane protein insertion machinery, chaperone, protein secretion; CHAPERONE
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	39.04 Å
Radius of gyration Rg (electron density) rg_electron	38.07 Å
Forward intensity I(0) i0	459057000.00
Molecular weight molecular_weight	185980.0 kDa
Excluded volume excluded_volume	237980 Å³
Envelope volume envelope_volume	322940 Å³
Hydration-shell volume shell_volume	68529 Å³
Envelope diameter envelope_diameter	131.4 Å
Shell Rg shell_rg	45.61 Å
Envelope Rg envelope_rg	37.72 Å
Shape Rg shape_rg	38.08 Å
Total Rg total_rg	38.55 Å
Total atoms total_atoms	26650
Residues n_residues	1698
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	124.1 Å
Rg (real space) rg_real	38.83 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	4.5910e+08
I(0) uncertainty (real space) i0_real_error	8.1880e+06
Rg (reciprocal space) rg_reciprocal	38.97 Å
I(0) (reciprocal space) i0_reciprocal	459100000.0000
Solution quality estimate total_estimate	0.8964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.6 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	76980000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.911

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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 SecY
Molecular weight formula_weight	50410.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y
Atom count atom_count	26650

VWNCERITISHRKQTMAKQPGLDFQSAKGGLGELKRRLLFVIGALIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISASIIIQLLTVVHPTLAEIKKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISLYLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGYGR

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein translocase subunit SecE
Molecular weight formula_weight	15248.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MHHHHHHDDDDKAMGANTEAQGSGRGLEAMKWVVVVALLLVAIVGNYLYRDIMLPLRALAVVILIAAAGGVALLTTKGKATVAFAREARTEVRKVIWPTRQETLHTTLIVAAVTAVMSLILWGLDGILVRLVSFITGLRF

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Protein-export membrane protein SecG
Molecular weight formula_weight	14326.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

VGTGWYSGSPGILYHWPEVLRIQELIMYEALLVVFLIVAIGLVGLIMLQQGKGADMGASFGAGASATLFGSSGSGNFMTRMTALLATLFFIISLVLGNINSNKTNKGSEWENLSAPAKTEQTQPAAPAKPTSDIPN

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Protein translocase subunit SecD
Molecular weight formula_weight	67688.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MHHHHHHMLNRYPLWKYVMLIVVIVIGLLYALPNLFGEDPAVQITGARGVAASEQTLIQVQKTLQEEKITAKSVALEEGAILARFDSTDTQLRAREALMGVMGDKYVVALNLAPATPRWLAAIHAEPMKLGLDLRGGVHFLMEVDMDTVLGKLQEQNIDSLRSDLREKGIPYTTVRKENNYGLSITFRDAKARDEAIAYLSKRHPDLVISSQGSNQLRAVMSDARLSEAREYAVQQNINILRNRVNQLGVAEPVVQRQGADRIVVELPGIQDTARAKEILGATATLEFRLVNTNVDQAAAASGRVPGDSEVKQTREGQPVVLYKRVILTGDHITDSTSSQDEYNQPQVNISLDSAGGNIMSNFTKDNIGKPMATLFVEYKDSGKKDANGRAVLVKQEEVINIANIQSRLGNSFRITGINNPNEARQLSLLLRAGALIAPIQIVEERTIGPTLGMQNIEQGLEACLAGLLVSILFMIIFYKKFGLIATSALIANLILIVGIMSLLPGATLSMPGIAGIVLTLAVAVDANVLINERIKEELSNGRTVQQAIDEGYRGAFSSIFDANITTLIKVIILYAVGTGAIKGFAITTGIGVATSMFTAIVGTRAIVNLLYGGKRVKKLSI

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Protein translocase subunit SecF
Molecular weight formula_weight	35413.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MAQEYTVEQLNHGRKVYDFMRWDYWAFGISGLLLIAAIVIMGVRGFNWGLDFTGGTVIEITLEKPAEIDVMRDALQKAGFEEPMLQNFGSSHDIMVRMPPAEGETGGQVLGSQVLKVINESTNQNAAVKRIEFVGPSVGADLAQTGAMALMAALLSILVYVGFRFEWRLAAGVVIALAHDVIITLGILSLFHIEIDLTIVASLMSVIGYSLNDSIVVSDRIRENFRKIRRGTPYEIFNVSLTQTLHRTLITSGTTLMVILMLYLFGGPVLEGFSLTMLIGVSIGTASSIYVASALALKLGMKREHMLQQKVEKEGADQPSILP

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Membrane protein insertase YidC
Molecular weight formula_weight	62658.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MDPSSRDSQRNLLVIALLFVSFMIWQAWEQDKNPQPQAQQTTQTTTTAAGSAADQGVPASGQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDAAYAAYAFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVDYGWLWFISQPLFKLLKWIHSFVGNWGFSIIIITFIVRGIMYPLTKAQYTSMAKMRMLQPKIQAMRERLGDDKQRISQEMMALYKAEKVNPLGGCFPLLIQMPIFLALYYMLMGSVELRQAPFALWIHDLSAQDPYYILPILMGVTMFFIQKMSPTTVTDPMQQKIMTFMPVIFTVFFLWFPSGLVLYYIVSNLVTIIQQQLIYRGLEKRGLHSREKKKSHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Resolution resolution	14.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	53648

fit	/app/data/saxs_computation/mg/5mg3/5mg3.fit
pddf	/app/data/pr_computation/mg/5mg3/5mg3.pr.out
profile	/app/data/saxs_computation/mg/5mg3/5mg3.dat

EM fitted model of bacterial holo-translocon

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

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

Protein-export membrane protein SecG

State in the Current Structure

Other States of the Same Protein in the Database

Protein translocase subunit SecD

State in the Current Structure

Other States of the Same Protein in the Database

Protein translocase subunit SecF

State in the Current Structure

Other States of the Same Protein in the Database

Membrane protein insertase YidC

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

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 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)