SAXSdb — 9qgy

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

Outer membrane protein TolC

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 × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain A； UniProt 23–493 Chain B； UniProt 23–493 Chain C； UniProt 23–493	Not recorded	Uncharacterized lipoprotein YbjP × 3 （P75818） Macrolide export protein MacA × 6 （P75830） Macrolide export ATP-binding/permease protein MacB × 2 （P75831） CL CHLORIDE ION × 3 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.48 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 9QGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EK9 2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN AND EFFLUX PUMP COMPONENT FROM ESCHERICHIA COLI Deposited 2000-03-07	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 × 3 PDB declaration: trimeric	Chain A 25–452（428 aa） Chain B 25–452（428 aa） Chain C 25–452（428 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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 7.4；298 K；PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.257
1TQQ Structure of TolC in complex with hexamminecobalt Deposited 2004-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 25–495（471 aa） Chain B 25–495（471 aa） Chain C 25–495（471 aa）	Not recorded	NCO COBALT HEXAMMINE(III) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% polyethylene glycol 2000 monomethyl ether, 10% polyethylene glycol 400, 10mM NaCl, 20mM MgCl2, 20mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.75 Å R-free 0.305
2VDD Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps Deposited 2007-10-04	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 × 3 PDB declaration: trimeric	Chain A 1–450（450 aa） Fragment：RESIDUES 1-450 Chain B 1–450（450 aa） Fragment：RESIDUES 1-450 Chain C 1–450（450 aa） Fragment：RESIDUES 1-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 3 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLISED FROM 0.1M HEPES 7.5, 5% ISOPROPANOL, 10% PEG4000	Resolution 3.30 Å R-free 0.295
2VDE Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps Deposited 2007-10-04	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 × 3 PDB declaration: trimeric	Chain A 1–450（450 aa） Fragment：RESIDUES 1-450 Chain B 1–450（450 aa） Fragment：RESIDUES 1-450 Chain C 1–450（450 aa） Fragment：RESIDUES 1-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；PROTEIN WAS CRYSTALLIZED FROM 0.1M CAPS PH10.5, 30% PEG400	Resolution 3.20 Å R-free 0.315
2WMZ Structure of a mutated TolC Deposited 2009-07-03	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 × 3 PDB declaration: trimeric	Chain A 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450 Chain B 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450 Chain C 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 3 PGE TRIETHYLENE GLYCOL × 5 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50 MM TRIS PH 8.2, 50 MM NACL, 14% PEG2000, 0.075% N-DODECYL-BETA-D-MALTOSIDE, 0.3% N-OCTYL BETA-D-GLUCOPYRANOSIDE	Resolution 2.90 Å R-free 0.301
2XMN High resolution snapshots of defined TolC open states present an iris- like movement of periplasmic entrance helices Deposited 2010-07-28	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 × 3 PDB declaration: trimeric	Chain A 23–450（428 aa） Fragment：RESIDUES 23-450 Chain B 23–450（428 aa） Fragment：RESIDUES 23-450 Chain C 23–450（428 aa） Fragment：RESIDUES 23-450	Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 3 LMT DODECYL-BETA-D-MALTOSIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；PH 7.4	Resolution 2.85 Å R-free 0.309
5NG5 multi-drug efflux; membrane transport; RND superfamily; Drug resistance Deposited 2017-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 1–493（493 aa） Chain F 1–493（493 aa） Chain I 1–493（493 aa）	Not recorded	5QF 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)	Resolution 6.50 Å
5NIK Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump Deposited 2017-03-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
5NIL Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section Deposited 2017-03-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å
5O66 Asymmetric AcrABZ-TolC Deposited 2017-06-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–493（493 aa） Chain B 1–493（493 aa） Chain C 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
5V5S multi-drug efflux; membrane transport; RND superfamily; Drug resistance Deposited 2017-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 23–464（442 aa） Chain B 23–464（442 aa） Chain C 23–464（442 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)	Resolution 6.50 Å
6WXH Colicin E1 fragment in nanodisc-embedded TolC Deposited 2020-05-10	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–493（493 aa） Chain B 1–493（493 aa） Chain C 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
6WXI Colicin E1 fragment in nanodisc-embedded TolC Deposited 2020-05-10	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–493（493 aa） Chain B 1–493（493 aa） Chain C 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
8ZAL EmrAB-TolC MFS-type tripartite multidrug efflux pump EA Deposited 2024-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 23–450（428 aa） Chain H 23–450（428 aa） Chain I 23–450（428 aa）	Mutation：V169L Mutation：V169L Mutation：V169L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8ZAR EmrAB-TolC MFS-type tripartite multidrug efflux pump FA Deposited 2024-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 1–493（493 aa） Chain H 1–493（493 aa） Chain I 1–493（493 aa）	Mutation：V191L Mutation：V191L Mutation：V191L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
9TG4 Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump Deposited 2025-11-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric	Chain A 23–493（471 aa） Chain B 23–493（471 aa） Chain C 23–493（471 aa）	Not recorded	CL CHLORIDE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9V52 Structure of TolC and YbjP closed state complex Deposited 2025-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C1 1–493（493 aa） Chain C2 1–493（493 aa） Chain C3 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.56 Å
9V53 Structure of TolC, YbjP, and AcrABZ complex Deposited 2025-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain C1 1–493（493 aa） Chain C2 1–493（493 aa） Chain C3 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.39 Å
9V55 Structure of TolC, YbjP, and AcrA complex Deposited 2025-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C1 1–493（493 aa） Chain C2 1–493（493 aa） Chain C3 1–493（493 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.26 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOLC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 23–493 Author chain B； PDBConstruct 1–471； UniProt 23–493 Author chain C； PDBConstruct 1–471； UniProt 23–493

Uncharacterized lipoprotein YbjP

Escherichia coli

UniProt P75818

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 × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain D； UniProt 19–171 Chain E； UniProt 19–171 Chain F； UniProt 19–171	Not recorded	Outer membrane protein TolC × 3 （P02930） Macrolide export protein MacA × 6 （P75830） Macrolide export ATP-binding/permease protein MacB × 2 （P75831） CL CHLORIDE ION × 3 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.48 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 9QGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9TG4 Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump Deposited 2025-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric	Chain P 28–171（144 aa） Chain Q 28–171（144 aa） Chain R 28–171（144 aa）	Not recorded	CL CHLORIDE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9V52 Structure of TolC and YbjP closed state complex Deposited 2025-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain P1 1–171（171 aa） Chain P2 1–171（171 aa） Chain P3 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.56 Å
9V53 Structure of TolC, YbjP, and AcrABZ complex Deposited 2025-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain P1 1–171（171 aa） Chain P2 1–171（171 aa） Chain P3 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.39 Å
9V55 Structure of TolC, YbjP, and AcrA complex Deposited 2025-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain P1 1–171（171 aa） Chain P2 1–171（171 aa） Chain P3 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.26 Å

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

View Construct and Data Evidence

UniProt name	YBJP_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–153； UniProt 19–171 Author chain E； PDBConstruct 1–153； UniProt 19–171 Author chain F； PDBConstruct 1–153； UniProt 19–171

Macrolide export protein MacA

Escherichia coli

UniProt P75830

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 × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain G； UniProt 1–371 Chain H； UniProt 1–371 Chain I； UniProt 1–371 Chain J； UniProt 1–371 Chain K； UniProt 1–371 Chain L； UniProt 1–371	Not recorded	Outer membrane protein TolC × 3 （P02930） Uncharacterized lipoprotein YbjP × 3 （P75818） Macrolide export ATP-binding/permease protein MacB × 2 （P75831） CL CHLORIDE ION × 3 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.48 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 9QGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FPP Crystal structure of E.coli MacA Deposited 2009-01-06	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 × 6 PDB declaration: hexameric	Chain A 31–371（341 aa） Chain B 31–371（341 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；1M potassium sodium tartrate tetrahydrate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.99 Å R-free 0.349
5NIK Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump Deposited 2017-03-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–371（371 aa） Chain E 1–371（371 aa） Chain F 1–371（371 aa） Chain G 1–371（371 aa） Chain H 1–371（371 aa） Chain I 1–371（371 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
5NIL Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section Deposited 2017-03-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–371（371 aa） Chain E 1–371（371 aa） Chain F 1–371（371 aa） Chain G 1–371（371 aa） Chain H 1–371（371 aa） Chain I 1–371（371 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MACA_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–371； UniProt 1–371 Author chain H； PDBConstruct 1–371； UniProt 1–371 Author chain I； PDBConstruct 1–371； UniProt 1–371 Author chain J； PDBConstruct 1–371； UniProt 1–371 Author chain K； PDBConstruct 1–371； UniProt 1–371 Author chain L； PDBConstruct 1–371； UniProt 1–371

Macrolide export ATP-binding/permease protein MacB

Escherichia coli

UniProt P75831

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 × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain M； UniProt 299–507 Chain N； UniProt 299–507	Not recorded	Outer membrane protein TolC × 3 （P02930） Uncharacterized lipoprotein YbjP × 3 （P75818） Macrolide export protein MacA × 6 （P75830） CL CHLORIDE ION × 3 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.48 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 9QGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LJ8 Structure of the E. coli MacB periplasmic domain (P21) Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 309–508（200 aa） Fragment：UNP residues 309-508	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；30% Pentaerythritol ethoxylate (15/4 EO/OH), 6% polyvinylpyrrolidone, 100mM HEPES pH 7.5	Resolution 1.95 Å R-free 0.228
5LJ8 Structure of the E. coli MacB periplasmic domain (P21) Deposited 2016-07-18	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 309–508（200 aa） Fragment：UNP residues 309-508	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；30% Pentaerythritol ethoxylate (15/4 EO/OH), 6% polyvinylpyrrolidone, 100mM HEPES pH 7.5	Resolution 1.95 Å R-free 0.228
5LJ9 Structure of the E. coli MacB ABC domain (C2221) Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；2.8 M sodium formate, 100 mM sodium acetate pH 4.6	Resolution 2.30 Å R-free 0.225
5LJ9 Structure of the E. coli MacB ABC domain (C2221) Deposited 2016-07-18	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 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；2.8 M sodium formate, 100 mM sodium acetate pH 4.6	Resolution 2.30 Å R-free 0.225
5LJ9 Structure of the E. coli MacB ABC domain (C2221) Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；2.8 M sodium formate, 100 mM sodium acetate pH 4.6	Resolution 2.30 Å R-free 0.225
5LJA Structure of the E. coli MacB ABC domain (P6122) Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–223（223 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；2.6 M sodium formate, 100 mM sodium acetate pH 4.6	Resolution 2.40 Å R-free 0.298
5NIK Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump Deposited 2017-03-24	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain J 1–648（648 aa） Chain K 1–648（648 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
5NIL Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section Deposited 2017-03-24	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain J 1–648（648 aa） Chain K 1–648（648 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å

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

View Construct and Data Evidence

UniProt name	MACB_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–209； UniProt 299–507 Author chain N； PDBConstruct 1–209； UniProt 299–507

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	9qgy
Deposition date deposition_date	2025-03-14
Structure title title	Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump
Keywords keywords	multi-drug efflux pump, MacAB-TolC, AcrABZ-TolC, type I secretion, lipoprotein, membrane protein assembly, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	83.56 Å
Radius of gyration Rg (electron density) rg_electron	85.04 Å
Forward intensity I(0) i0	3097850000.00
Molecular weight molecular_weight	461900.0 kDa
Excluded volume excluded_volume	575720 Å³
Envelope volume envelope_volume	945870 Å³
Hydration-shell volume shell_volume	103740 Å³
Envelope diameter envelope_diameter	291.9 Å
Shell Rg shell_rg	63.00 Å
Envelope Rg envelope_rg	83.44 Å
Shape Rg shape_rg	85.09 Å
Total Rg total_rg	84.53 Å
Total atoms total_atoms	64967
Residues n_residues	4198
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	227.8 Å
Rg (real space) rg_real	78.91 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	2.9730e+09
I(0) uncertainty (real space) i0_real_error	5.5690e+07
Rg (reciprocal space) rg_reciprocal	78.58 Å
I(0) (reciprocal space) i0_reciprocal	3054000000.0000
Solution quality estimate total_estimate	0.8252
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	60.0 Å
Skewness Skewness skewness	0.432
Kurtosis Kurtosis kurtosis	-0.920
Angular range angular_range	— – 0.0950 Å⁻¹
Current regularization parameter α current_alpha	0.8833
Highest regularization parameter α highest_alpha	523100000.0000
Real-space data points n_real_points	20
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.669; Stabil: 0.960; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein TolC
Molecular weight formula_weight	51495.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	64989

ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN

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	Uncharacterized lipoprotein YbjP
Molecular weight formula_weight	17004.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

CTTVTPAYKDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENR

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	Macrolide export protein MacA
Molecular weight formula_weight	40672.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

MKKRKTVKKRYVIALVIVIAGLITLWRILNAPVPTYQTLIVRPGDLQQSVLATGKLDALRKVDVGAQVSGQLKTLSVAIGDKVKKDQLLGVIDPEQAENQIKEVEATLMELRAQRQQAEAELKLARVTYSRQQRLAQTKAVSQQDLDTAATEMAVKQAQIGTIDAQIKRNQASLDTAKTNLDYTRIVAPMAGEVTQITTLQGQTVIAAQQAPNILTLADMSAMLVKAQVSEADVIHLKPGQKAWFTVLGDPLTRYEGQIKDVLPTPEKVNDAIFYYARFEVPNPNGLLRLDMTAQVHIQLTDVKNVLTIPLSALGDPVGDNRYKVKLLRNGETREREVTIGARNDTDVEIVKGLEAGDEVVIGEAKPGAAQ

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	Macrolide export ATP-binding/permease protein MacB
Molecular weight formula_weight	23354.3 kDa
EC 编号 ec_number	7.6.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

MVLADIRSIGTNTIDVYPGKDFGDDDPQYQQALKYDDLIAIQKQPWVASATPAVSQNLRLRYNNVDVAASANGVSGDYFNVYGMTFSEGNTFNQEQLNGRAQVVVLDSNTRRQLFPHKADVVGEVILVGNMPARVIGVAEEKQSMFGSSKVLRVWLPYSTMSGRVMGQSWLNSITVRVKEGFDSAEAEQQLTRLLSLRHGKKDFFTWNM

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 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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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	2.480 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.48 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	233775

fit	/app/data/saxs_computation/qg/9qgy/9qgy.fit
pddf	/app/data/pr_computation/qg/9qgy/9qgy.pr.out
profile	/app/data/saxs_computation/qg/9qgy/9qgy.dat

Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump

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

Outer membrane protein TolC

State in the Current Structure

Other States of the Same Protein in the Database

Uncharacterized lipoprotein YbjP

State in the Current Structure

Other States of the Same Protein in the Database

Macrolide export protein MacA

State in the Current Structure

Other States of the Same Protein in the Database

Macrolide export ATP-binding/permease protein MacB

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

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)