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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Uncharacterized lipoprotein YbjP × 3 （P75818） Multidrug efflux pump subunit AcrA × 6 （P0AE06）	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Outer membrane protein TolC × 3 （P02930） Multidrug efflux pump subunit AcrA × 6 （P0AE06）	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Outer membrane protein TolC × 3 （P02930） Uncharacterized lipoprotein YbjP × 3 （P75818）	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9v55__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9v55__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9v55__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	79.62 Å
Rg (electron density)	80.73 Å
Total Rg	80.58 Å
Atom count	29061
Residues	3816
Excluded volume	513830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9v55__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism 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

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism 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

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

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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Method resolution_method	—
颗粒数 num_particles	17043

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9v55__assembly_1__model_1

9v55__assembly_1__model_1 | I(q)

9v55__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (2)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Uncharacterized lipoprotein YbjP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Multidrug efflux pump subunit AcrA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9v55__assembly_1__model_1

9v55__assembly_1__model_1 | I(q)

9v55__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (2)