2wcd

Crystal structure of the assembled cytolysin A pore

Method: X-RAY DIFFRACTION

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

HEMOLYSIN E, CHROMOSOMAL

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 24	ETHYL MERCURY ION × 48	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	ETHYL MERCURY ION × 24	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 12	ETHYL MERCURY ION × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLYE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–309； UniProt 2–303 Author chain B； PDBConstruct 8–309； UniProt 2–303 Author chain C； PDBConstruct 8–309； UniProt 2–303 Author chain D； PDBConstruct 8–309； UniProt 2–303 Author chain E； PDBConstruct 8–309； UniProt 2–303 Author chain F； PDBConstruct 8–309； UniProt 2–303 Author chain G； PDBConstruct 8–309； UniProt 2–303 Author chain H； PDBConstruct 8–309； UniProt 2–303 Author chain I； PDBConstruct 8–309； UniProt 2–303 Author chain J； PDBConstruct 8–309； UniProt 2–303 Author chain K； PDBConstruct 8–309； UniProt 2–303 Author chain L； PDBConstruct 8–309； UniProt 2–303 Author chain M； PDBConstruct 8–309； UniProt 2–303 Author chain N； PDBConstruct 8–309； UniProt 2–303 Author chain O； PDBConstruct 8–309； UniProt 2–303 Author chain P； PDBConstruct 8–309； UniProt 2–303 Author chain Q； PDBConstruct 8–309； UniProt 2–303 Author chain R； PDBConstruct 8–309； UniProt 2–303 Author chain S； PDBConstruct 8–309； UniProt 2–303 Author chain T； PDBConstruct 8–309； UniProt 2–303 Author chain U； PDBConstruct 8–309； UniProt 2–303 Author chain V； PDBConstruct 8–309； UniProt 2–303 Author chain W； PDBConstruct 8–309； UniProt 2–303 Author chain X； PDBConstruct 8–309； UniProt 2–303

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	2wcd
Deposition date deposition_date	2009-03-11
Structure title title	Crystal structure of the assembled cytolysin A pore
Keywords keywords	;CYTOLYTIC PROTEIN, PORE-FORMING TOXIN, TRANSMEMBRANE PORE, TOXIN, MEMBRANE, SECRETED, CYTOLYSIS, PERIPLASM, HEMOLYSIS, TRANSMEMBRANE, DISULFIDE BOND ;; 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.

2wcd__assembly_1__model_1

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

Download this curve (.dat)

2wcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	80.76 Å
Rg (electron density)	82.69 Å
Total Rg	81.60 Å
Atom count	53832
Residues	6840
Excluded volume	970590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wcd__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wcd__assembly_2__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wcd__assembly_3__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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	2wcdA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdN00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdO00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdP00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdQ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdR00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdS00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdT00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdU00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdV00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdW00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wcdX00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1170 — Hemolysin E; Chain: A;
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	111.430 Å
Unit-cell length b length_b	114.410 Å
Unit-cell length c length_c	270.550 Å
Unit-cell angle α angle_alpha	94.44 °
Unit-cell angle β angle_beta	85.92 °
Unit-cell angle γ angle_gamma	102.55 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	49.370 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2440

Description description	HEMOLYSIN E, CHROMOSOMAL
Molecular weight formula_weight	34624.3 kDa
Source method src_method	man
Copy count entity_count	24

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Atom count atom_count	53832

Crystal structure of the assembled cytolysin A pore

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

HEMOLYSIN E, CHROMOSOMAL

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

2wcd__assembly_1__model_1

2wcd__assembly_1__model_1 | I(q)

2wcd__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Description description	ETHYL MERCURY ION
Molecular weight formula_weight	229.7 kDa
Source method src_method	syn
Copy count entity_count	48

Crystal structure of the assembled cytolysin A pore

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

HEMOLYSIN E, CHROMOSOMAL

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

2wcd__assembly_1__model_1

2wcd__assembly_1__model_1 | I(q)

2wcd__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)