9qgy

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

Method: ELECTRON MICROSCOPY

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Uncharacterized lipoprotein YbjP × 3 （P75818） Macrolide export protein MacA × 6 （P75830） Macrolide export ATP-binding/permease protein MacB × 2 （P75831） CHLORIDE ION × 3 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3 water × 5	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 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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Outer membrane protein TolC × 3 （P02930） Macrolide export protein MacA × 6 （P75830） Macrolide export ATP-binding/permease protein MacB × 2 （P75831） CHLORIDE ION × 3 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3 water × 5	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 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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Outer membrane protein TolC × 3 （P02930） Uncharacterized lipoprotein YbjP × 3 （P75818） Macrolide export ATP-binding/permease protein MacB × 2 （P75831） CHLORIDE ION × 3 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Outer membrane protein TolC × 3 （P02930） Uncharacterized lipoprotein YbjP × 3 （P75818） Macrolide export protein MacA × 6 （P75830） CHLORIDE ION × 3 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

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. 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.

9qgy__assembly_1__model_1

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

Download this curve (.dat)

9qgy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qgy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	83.56 Å
Rg (electron density)	85.04 Å
Total Rg	84.53 Å
Atom count	64967
Residues	4198
Excluded volume	575720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qgy__assembly_1__model_1`	14-meric （14）	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 (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

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism 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

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism 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

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism 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

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism 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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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Method resolution_method	—
颗粒数 num_particles	233775

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

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

Macrolide export protein MacA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Macrolide export ATP-binding/permease protein MacB

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

9qgy__assembly_1__model_1

9qgy__assembly_1__model_1 | I(q)

9qgy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)