4p2c

Complex of Shiga toxin 2e with a neutralizing single-domain antibody

Method: X-RAY DIFFRACTION

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

Shiga toxin 2e, subunit A

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Shiga toxin 2e, subunit B × 5 （Q47644） Nanobody 1, Anti-F4+ETEC bacteria VHH variable region × 5 （R9VYW2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7WUF4_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 23–319

Shiga toxin 2e, subunit B

Escherichia coli

UniProt Q47644

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Shiga toxin 2e, subunit A × 1 （Q7WUF4） Nanobody 1, Anti-F4+ETEC bacteria VHH variable region × 5 （R9VYW2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q47644_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–68； UniProt 20–87 Author chain C； PDBConstruct 1–68； UniProt 20–87 Author chain D； PDBConstruct 1–68； UniProt 20–87 Author chain E； PDBConstruct 1–68； UniProt 20–87 Author chain F； PDBConstruct 1–68； UniProt 20–87

Nanobody 1, Anti-F4+ETEC bacteria VHH variable region

Lama glama

UniProt R9VYW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Shiga toxin 2e, subunit A × 1 （Q7WUF4） Shiga toxin 2e, subunit B × 5 （Q47644）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R9VYW2_LAMGL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–122； UniProt 1–121 Author chain H； PDBConstruct 1–122； UniProt 1–121 Author chain I； PDBConstruct 1–122； UniProt 1–121 Author chain J； PDBConstruct 1–122； UniProt 1–121 Author chain K； PDBConstruct 1–122； UniProt 1–121

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	4p2c
Deposition date deposition_date	2014-03-03
Structure title title	Complex of Shiga toxin 2e with a neutralizing single-domain antibody
Keywords keywords	Nanobody, Toxin, Complex, Lectin; 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.

4p2c__assembly_1__model_1

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

Download this curve (.dat)

4p2c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4p2c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.02 Å
Rg (electron density)	35.51 Å
Total Rg	35.92 Å
Atom count	9541
Residues	1228
Excluded volume	167640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4p2c__assembly_1__model_1`	undecameric （11）	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	Shiga toxin 2e, subunit A
Molecular weight formula_weight	33012.0 kDa
Mutation mutation	Y99S, E189Q, K296T, P313S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9541

QEFTIDFSTQQSYVSSLNSIRTAISTPLEHISQGATSVSVINHTPPGSYISVGIRGLDVYQERFDHLRLIIERNNLSVAGFVNTTTNTFYRFSDFAHISLPGVTTISMTTDSSYTTPQRVAALERSGMQVSRHSLVSSYLALMEFSGNTMTREASRAVLRFVTVTAQALRFRQIQREFRQALSETAPVYTMTPEDVDLTLNWGRISNVLPEYRGEAGVRVGRISFNNISAILGTVAVILNCHHQGARSVRAVNEESQPECQITGDRPVIKITNTLWESNTAAAFLNRKSQSLYTTGE

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	Shiga toxin 2e, subunit B
Molecular weight formula_weight	7590.5 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN

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	Nanobody 1, Anti-F4+ETEC bacteria VHH variable region
Molecular weight formula_weight	14196.6 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

QVQLQESGGGLVQAGGSLRLSCAVSGSIFRLSTMGWYRQAPGKQREFVASITSYGDTNYRDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANIEAGTYYGPGRDYWGQGTQVTVSSHHHHHH

Source Source

Source organism organism	Lama glama
Common name common_name	Llama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4p2ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.2 — Shiga toxin, A-chain

Domain ID domain_id	d4p2cb_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d4p2cc_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d4p2cd_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d4p2ce_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d4p2cf_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d4p2cg_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4p2ch_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4p2ci_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4p2cj1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4p2cj2
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	d4p2ck_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (12 domains)

Domain ID domain_id	4p2cA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	4p2cA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

Domain ID domain_id	4p2cB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4p2cC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4p2cD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4p2cE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4p2cF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4p2cG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4p2cH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4p2cI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4p2cJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4p2cK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	191.838 Å
Unit-cell length b length_b	88.192 Å
Unit-cell length c length_c	100.664 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	20

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

Resolution resolution	2.818 Å
Low-resolution limit resolution_low	43.714 Å
R factor r_factor	0.1898
R_work r_work	0.1865
R_free r_free	0.2530

Complex of Shiga toxin 2e with a neutralizing single-domain antibody

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

Shiga toxin 2e, subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Shiga toxin 2e, subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Nanobody 1, Anti-F4+ETEC bacteria VHH variable region

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

4p2c__assembly_1__model_1

4p2c__assembly_1__model_1 | I(q)

4p2c__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 (3)

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

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Complex of Shiga toxin 2e with a neutralizing single-domain antibody

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

Shiga toxin 2e, subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Shiga toxin 2e, subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nanobody 1, Anti-F4+ETEC bacteria VHH variable region

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

4p2c__assembly_1__model_1

4p2c__assembly_1__model_1 | I(q)

4p2c__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 (3)

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

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)