SAXSdb — 9v55

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

Outer membrane protein TolC

Escherichia coli K-12

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C1； UniProt 1–493 Chain C2； UniProt 1–493 Chain C3； UniProt 1–493	Not recorded	Uncharacterized lipoprotein YbjP × 3 （P75818） Multidrug efflux pump subunit AcrA × 6 （P0AE06）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.26 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 9V55	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 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 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 construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 oligomeric state 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 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 oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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 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 mutation/modification Different oligomeric state 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
9QGY Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump Deposited 2025-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-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 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
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 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 oligomeric state 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 oligomeric state 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

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 C1； PDBConstruct 1–493； UniProt 1–493 Author chain C2； PDBConstruct 1–493； UniProt 1–493 Author chain C3； PDBConstruct 1–493； UniProt 1–493

Uncharacterized lipoprotein YbjP

Escherichia coli K-12

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain P1； UniProt 1–171 Chain P2； UniProt 1–171 Chain P3； UniProt 1–171	Not recorded	Outer membrane protein TolC × 3 （P02930） Multidrug efflux pump subunit AcrA × 6 （P0AE06）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.26 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 9V55	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9QGY Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump Deposited 2025-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain D 19–171（153 aa） Chain E 19–171（153 aa） Chain F 19–171（153 aa）	Not recorded	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
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 oligomeric state 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 oligomeric state 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

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 P1； PDBConstruct 1–171； UniProt 1–171 Author chain P2； PDBConstruct 1–171； UniProt 1–171 Author chain P3； PDBConstruct 1–171； UniProt 1–171

Multidrug efflux pump subunit AcrA

Escherichia coli K-12

UniProt P0AE06

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A1； UniProt 1–397 Chain A2； UniProt 1–397 Chain A3； UniProt 1–397 Chain a1； UniProt 1–397 Chain a2； UniProt 1–397 Chain a3； UniProt 1–397	Not recorded	Outer membrane protein TolC × 3 （P02930） Uncharacterized lipoprotein YbjP × 3 （P75818）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.26 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 9V55	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2F1M Conformational flexibility in the multidrug efflux system protein AcrA Deposited 2005-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 45–312（268 aa） Fragment：residues 45-312 Chain B 45–312（268 aa） Fragment：residues 45-312	Mutation：F223M, L224M, L287M, L288M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F223M, L224M, L287M, L288M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；277 K；30% 2-methyl-2,4-pentadiol (MPD), 20 mM MgCl2, 100 mM citrate pH 5.4, 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.40	Resolution 2.71 Å R-free 0.275
2F1M Conformational flexibility in the multidrug efflux system protein AcrA Deposited 2005-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 45–312（268 aa） Fragment：residues 45-312 Chain D 45–312（268 aa） Fragment：residues 45-312	Mutation：F223M, L224M, L287M, L288M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F223M, L224M, L287M, L288M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；277 K；30% 2-methyl-2,4-pentadiol (MPD), 20 mM MgCl2, 100 mM citrate pH 5.4, 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.40	Resolution 2.71 Å R-free 0.275
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 A 25–397（373 aa） Chain B 25–397（373 aa） Chain D 25–397（373 aa） Chain E 25–397（373 aa） Chain G 25–397（373 aa） Chain H 25–397（373 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
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 D 1–397（397 aa） Chain E 1–397（397 aa） Chain F 1–397（397 aa） Chain G 1–397（397 aa） Chain H 1–397（397 aa） Chain I 1–397（397 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
9V53 Structure of TolC, YbjP, and AcrABZ complex Deposited 2025-05-25	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A1 1–397（397 aa） Chain A2 1–397（397 aa） Chain A3 1–397（397 aa） Chain a1 1–397（397 aa） Chain a2 1–397（397 aa） Chain a3 1–397（397 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

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

View Construct and Data Evidence

UniProt name	ACRA_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A1； PDBConstruct 1–397； UniProt 1–397 Author chain A2； PDBConstruct 1–397； UniProt 1–397 Author chain A3； PDBConstruct 1–397； UniProt 1–397 Author chain a1； PDBConstruct 1–397； UniProt 1–397 Author chain a2； PDBConstruct 1–397； UniProt 1–397 Author chain a3； PDBConstruct 1–397； UniProt 1–397

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	9v55
Deposition date deposition_date	2025-05-25
Structure title title	Structure of TolC, YbjP, and AcrA complex
Keywords keywords	Multidrug efflux pump, TolC, YbjP, AcrA, AcrB, lipoprotein, antibiotic resistance, Gram-negative, 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	79.62 Å
Radius of gyration Rg (electron density) rg_electron	80.73 Å
Forward intensity I(0) i0	2503220000.00
Molecular weight molecular_weight	412770.0 kDa
Excluded volume excluded_volume	513830 Å³
Envelope volume envelope_volume	887490 Å³
Hydration-shell volume shell_volume	102210 Å³
Envelope diameter envelope_diameter	285.1 Å
Shell Rg shell_rg	61.62 Å
Envelope Rg envelope_rg	80.36 Å
Shape Rg shape_rg	80.67 Å
Total Rg total_rg	80.58 Å
Total atoms total_atoms	29061
Residues n_residues	3816
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	214.7 Å
Rg (real space) rg_real	75.64 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	2.4230e+09
I(0) uncertainty (real space) i0_real_error	4.8790e+07
Rg (reciprocal space) rg_reciprocal	76.18 Å
I(0) (reciprocal space) i0_reciprocal	2480000000.0000
Solution quality estimate total_estimate	0.8621
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	64.4 Å
Skewness Skewness skewness	0.407
Kurtosis Kurtosis kurtosis	-0.816
Angular range angular_range	— – 0.1000 Å⁻¹
Current regularization parameter α current_alpha	0.1867
Highest regularization parameter α highest_alpha	225900000.0000
Real-space data points n_real_points	21
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.845; Stabil: 0.978; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.008

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein TolC
Molecular weight formula_weight	53783.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C1,C2,C3
Atom count atom_count	29061

MKKLLPILIGLSLSGFSSLSQAENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Uncharacterized lipoprotein YbjP
Molecular weight formula_weight	19013.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P1,P2,P3

MRYSKLTMLIPCALLLSACTTVTPAYKDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENR

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Multidrug efflux pump subunit AcrA
Molecular weight formula_weight	42237.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A1,A2,A3,a2,a1,a3

MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQEYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

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8. Citations (2)

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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	triclinic

Resolution resolution	3.26 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	17043

fit	/app/data/saxs_computation/v5/9v55/9v55.fit
pddf	/app/data/pr_computation/v5/9v55/9v55.pr.out
profile	/app/data/saxs_computation/v5/9v55/9v55.dat

Structure of TolC, YbjP, and AcrA complex

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

Multidrug efflux pump subunit AcrA

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 (3)

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

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)