3jqo

Crystal structure of the outer membrane complex of a type IV secretion system

Method: X-RAY DIFFRACTION

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

TraF protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	TraO protein × 14 （Q46704） TraN protein × 14 （Q46702） (4S)-2-METHYL-2,4-PENTANEDIOL × 3 LAURYL DIMETHYLAMINE-N-OXIDE × 1 water × 42	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q46705_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–227； UniProt 160–386 Author chain D； PDBConstruct 1–227； UniProt 160–386 Author chain G； PDBConstruct 1–227； UniProt 160–386 Author chain J； PDBConstruct 1–227； UniProt 160–386 Author chain M； PDBConstruct 1–227； UniProt 160–386 Author chain P； PDBConstruct 1–227； UniProt 160–386 Author chain S； PDBConstruct 1–227； UniProt 160–386 Author chain V； PDBConstruct 1–227； UniProt 160–386 Author chain Y； PDBConstruct 1–227； UniProt 160–386 Author chain b； PDBConstruct 1–227； UniProt 160–386 Author chain e； PDBConstruct 1–227； UniProt 160–386 Author chain h； PDBConstruct 1–227； UniProt 160–386 Author chain k； PDBConstruct 1–227； UniProt 160–386 Author chain n； PDBConstruct 1–227； UniProt 160–386

TraO protein

Escherichia coli

UniProt Q46704

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	TraF protein × 14 （Q46705） TraN protein × 14 （Q46702） (4S)-2-METHYL-2,4-PENTANEDIOL × 3 LAURYL DIMETHYLAMINE-N-OXIDE × 1 water × 42	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q46704_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–135； UniProt 160–294 Author chain E； PDBConstruct 1–135； UniProt 160–294 Author chain H； PDBConstruct 1–135； UniProt 160–294 Author chain K； PDBConstruct 1–135； UniProt 160–294 Author chain N； PDBConstruct 1–135； UniProt 160–294 Author chain Q； PDBConstruct 1–135； UniProt 160–294 Author chain T； PDBConstruct 1–135； UniProt 160–294 Author chain W； PDBConstruct 1–135； UniProt 160–294 Author chain Z； PDBConstruct 1–135； UniProt 160–294 Author chain c； PDBConstruct 1–135； UniProt 160–294 Author chain f； PDBConstruct 1–135； UniProt 160–294 Author chain i； PDBConstruct 1–135； UniProt 160–294 Author chain l； PDBConstruct 1–135； UniProt 160–294 Author chain o； PDBConstruct 1–135； UniProt 160–294

TraN protein

Escherichia coli

UniProt Q46702

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	TraF protein × 14 （Q46705） TraO protein × 14 （Q46704） (4S)-2-METHYL-2,4-PENTANEDIOL × 3 LAURYL DIMETHYLAMINE-N-OXIDE × 1 water × 42	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q46702_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–34； UniProt 15–48 Author chain F； PDBConstruct 1–34； UniProt 15–48 Author chain I； PDBConstruct 1–34； UniProt 15–48 Author chain L； PDBConstruct 1–34； UniProt 15–48 Author chain O； PDBConstruct 1–34； UniProt 15–48 Author chain R； PDBConstruct 1–34； UniProt 15–48 Author chain U； PDBConstruct 1–34； UniProt 15–48 Author chain X； PDBConstruct 1–34； UniProt 15–48 Author chain a； PDBConstruct 1–34； UniProt 15–48 Author chain d； PDBConstruct 1–34； UniProt 15–48 Author chain g； PDBConstruct 1–34； UniProt 15–48 Author chain j； PDBConstruct 1–34； UniProt 15–48 Author chain m； PDBConstruct 1–34； UniProt 15–48 Author chain p； PDBConstruct 1–34； UniProt 15–48

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	3jqo
Deposition date deposition_date	2009-09-07
Structure title title	Crystal structure of the outer membrane complex of a type IV secretion system
Keywords keywords	Helical outer membrane TM, outer membrane protein complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3jqo__assembly_1__model_1

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

Download this curve (.dat)

3jqo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jqo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	64.00 Å
Rg (electron density)	63.68 Å
Total Rg	63.47 Å
Atom count	37552
Residues	4797
Excluded volume	665330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jqo__assembly_1__model_1`	42-meric （42）	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 (6)

Entity 1 Entity 1 polymer

Description description	TraF protein
Molecular weight formula_weight	24293.1 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J,M,P,S,V,Y,b,e,h,k,n
Atom count atom_count	38842

SNSPGAQPQDNETSEGSSALAKNLTPARLKASRAGVMANPSLTVPKGKMIPCGTGTELDTTVPGQVSCRVSQDVYSADGLVRLIDKGSWVDGQITGGIKDGQARVFVLWERIRNDQDGTIVNIDSAGTNSLGSAGIPGQVDAHMWERLRGAIMISLFSDTLTALVNQTQSNNIQYNSTENSGGQLASEALRSYMSIPPTLYDQQGDAVSIFVARDLDFSGVYTLADN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TraO protein
Molecular weight formula_weight	15323.8 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K,N,Q,T,W,Z,c,f,i,l,o

SAADKKRITQKLKQTAFAGAKNYQYVMSEQPEMRSIQPVHVWDNYRFTRFEFPANAELPQVYMISASGKETLPNSHVVGENRNIIEVETVAKEWRIRLGDKVVGVRNNNFAPGRGAVATGTASPDVRRVQIGEDN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	TraN protein
Molecular weight formula_weight	3635.9 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L,O,R,U,X,a,d,g,j,m,p

CSSGHKPPPEPDWSNTVPVNKTIPVDTQGGRNES

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1290

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6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id	3jqoA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoG01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoJ01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoM01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoP01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoQ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoS01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoT00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoV01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoW00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoY01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoZ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqob01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoc00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoe01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqof00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqoh01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoi00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqok01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqol00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

Domain ID domain_id	3jqon01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	260 — Type IV secretion system, VirB10/TraB/TrbI

Domain ID domain_id	3jqoo00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2500 —

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Unit-cell length a length_a	202.400 Å
Unit-cell length b length_b	211.630 Å
Unit-cell length c length_c	203.440 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	56

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	52.910 Å
R factor r_factor	0.2288
R_work r_work	0.2273
R_free r_free	0.2594

Crystal structure of the outer membrane complex of a type IV secretion system

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

TraF protein

State in the Current Structure

Other States of the Same Protein in the Database

TraO protein

State in the Current Structure

Other States of the Same Protein in the Database

TraN protein

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

3jqo__assembly_1__model_1

3jqo__assembly_1__model_1 | I(q)

3jqo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

7. Citations (1)

Crystal structure of the outer membrane complex of a type IV secretion system

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

TraF protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TraO protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TraN protein

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

3jqo__assembly_1__model_1

3jqo__assembly_1__model_1 | I(q)

3jqo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

7. Citations (1)