2a6q

Crystal structure of YefM-YoeB complex

Method: X-RAY DIFFRACTION

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

Antitoxin yefM

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Toxin yoeB × 1 （P69348） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Toxin yoeB × 1 （P69348） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Toxin yoeB × 2 （P69348） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YEFM_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–86； UniProt 1–83 Author chain B； PDBConstruct 4–86； UniProt 1–83 Author chain C； PDBConstruct 4–86； UniProt 1–83 Author chain D； PDBConstruct 4–86； UniProt 1–83

Toxin yoeB

Escherichia coli

UniProt P69348

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Antitoxin yefM × 2 （P69346） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Antitoxin yefM × 2 （P69346） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Antitoxin yefM × 4 （P69346） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YOEB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–84； UniProt 1–84 Author chain F； PDBConstruct 1–84； UniProt 1–84

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	2a6q
Deposition date deposition_date	2005-07-04
Structure title title	Crystal structure of YefM-YoeB complex
Keywords keywords	YoeB, YefM, toxin, antitoxin, addiction modules, RNase, inhibitor, TOXIN INHIBITOR-TOXIN COMPLEX; TOXIN INHIBITOR/TOXIN
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.

2a6q__assembly_1__model_1

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

Download this curve (.dat)

2a6q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a6q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.05 Å
Rg (electron density)	20.19 Å
Total Rg	21.04 Å
Atom count	1844
Residues	228
Excluded volume	32696 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a6q__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2a6q__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2a6q__assembly_3__model_1`	hexameric （6）	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	Antitoxin yefM
Molecular weight formula_weight	9610.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3841

GPHMRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKDIIE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Toxin yoeB
Molecular weight formula_weight	10233.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2a6qa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.1 — YefM-like

Domain ID domain_id	d2a6qa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2a6qb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.1 — YefM-like

Domain ID domain_id	d2a6qb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2a6qc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.1 — YefM-like

Domain ID domain_id	d2a6qc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2a6qd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.1 — YefM-like

Domain ID domain_id	d2a6qd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2a6qe1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.1 — YoeB/Txe-like

Domain ID domain_id	d2a6qf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.1 — YoeB/Txe-like

CATH v4.4 (8 domains)

Domain ID domain_id	2a6qA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	2a6qA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	2a6qB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	2a6qC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	2a6qC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	2a6qD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	2a6qE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	2a6qF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

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Unit-cell length a length_a	88.485 Å
Unit-cell length b length_b	88.485 Å
Unit-cell length c length_c	135.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	29.190 Å
R factor r_factor	0.2250
R_work r_work	0.2240
R_free r_free	0.2540

Crystal structure of YefM-YoeB complex

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

Antitoxin yefM

State in the Current Structure

Other States of the Same Protein in the Database

Toxin yoeB

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

2a6q__assembly_1__model_1

2a6q__assembly_1__model_1 | I(q)

2a6q__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of YefM-YoeB complex

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

Antitoxin yefM

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Toxin yoeB

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

2a6q__assembly_1__model_1

2a6q__assembly_1__model_1 | I(q)

2a6q__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. Citations (1)