1l2w

Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE

Method: X-RAY DIFFRACTION

▼

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

Outer membrane virulence protein yopE

Yersinia pseudotuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	YopE regulator × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	YopE regulator × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	YopE regulator × 2 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	YopE regulator × 2 water × 3	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	YopE regulator × 4 water × 6	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 6	YopE regulator × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YOPE_YERPS
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–69； UniProt 17–85 Author chain J； PDBConstruct 1–69； UniProt 17–85 Author chain K； PDBConstruct 1–69； UniProt 17–85 Author chain L； PDBConstruct 1–69； UniProt 17–85

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1l2w
Deposition date deposition_date	2002-02-25
Structure title title	Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE
Keywords keywords	CHAPERONE AND VIRULENCE PROTEIN, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1l2w__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1l2w__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1l2w__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.79 Å
Rg (electron density)	19.65 Å
Total Rg	20.57 Å
Atom count	2315
Residues	294
Excluded volume	41095 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l2w__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1l2w__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1l2w__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1l2w__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1l2w__assembly_5__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1l2w__assembly_6__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	YopE regulator
Molecular weight formula_weight	13843.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	9594

MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSSL

Source Source

Source organism organism	Yersinia pseudotuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	633
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Outer membrane virulence protein yopE
Molecular weight formula_weight	7278.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L

VSGSSSVGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMFSEGSHKP

Source Source

Source organism organism	Yersinia pseudotuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	633
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	362

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1l2wa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2we_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1l2wi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
Superfamily Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
Family Family family	d.184.1.2 — Type III secretory system effector

Domain ID domain_id	d1l2wj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
Superfamily Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
Family Family family	d.184.1.2 — Type III secretory system effector

Domain ID domain_id	d1l2wk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
Superfamily Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
Family Family family	d.184.1.2 — Type III secretory system effector

Domain ID domain_id	d1l2wl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.184 — Non-globular alpha+beta subunits of globular proteins
Superfamily Superfamily superfamily	d.184.1 — Non-globular alpha+beta subunits of globular proteins
Family Family family	d.184.1.2 — Type III secretory system effector

CATH v4.4 (8 domains)

Domain ID domain_id	1l2wA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1l2wH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	72.845 Å
Unit-cell length b length_b	73.352 Å
Unit-cell length c length_c	74.263 Å
Unit-cell angle α angle_alpha	103.37 °
Unit-cell angle β angle_beta	109.18 °
Unit-cell angle γ angle_gamma	107.36 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2510
R_free r_free	0.2750

Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE

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

Outer membrane virulence protein yopE

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

1l2w__assembly_2__model_1

1l2w__assembly_2__model_1 | I(q)

1l2w__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE

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

Outer membrane virulence protein yopE

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

1l2w__assembly_2__model_1

1l2w__assembly_2__model_1 | I(q)

1l2w__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)