4p1x

Crystal structure of staphylococcal LUK prepore

Method: X-RAY DIFFRACTION

▼

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

Gamma-hemolysin component C

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Gamma-hemolysin component B × 4 （Q931F3） (4S)-2-METHYL-2,4-PENTANEDIOL × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLGC_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 11–296； UniProt 30–315 Author chain D； PDBConstruct 11–296； UniProt 30–315 Author chain F； PDBConstruct 11–296； UniProt 30–315 Author chain H； PDBConstruct 11–296； UniProt 30–315

Gamma-hemolysin component B

Staphylococcus aureus

UniProt Q931F3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Gamma-hemolysin component C × 4 （Q99RL1） (4S)-2-METHYL-2,4-PENTANEDIOL × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q931F3_STAAM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 11–309； UniProt 27–325 Author chain C； PDBConstruct 11–309； UniProt 27–325 Author chain E； PDBConstruct 11–309； UniProt 27–325 Author chain G； PDBConstruct 11–309； UniProt 27–325

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	4p1x
Deposition date deposition_date	2014-02-28
Structure title title	Crystal structure of staphylococcal LUK prepore
Keywords keywords	pore forming toxin, TOXIN; TOXIN
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.

4p1x__assembly_1__model_1

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

Download this curve (.dat)

4p1x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4p1x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.12 Å
Rg (electron density)	41.24 Å
Total Rg	41.72 Å
Atom count	33770
Residues	2092
Excluded volume	302840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4p1x__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Gamma-hemolysin component C
Molecular weight formula_weight	33816.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H
Atom count atom_count	34827

MGHHHHHHAMANDTEDIGKGSDIEIIKRTEDKTSNKWGVTQNIQFDFVKDKKYNKDALILKMQGFISSRTTYYNYKKTNHVKAMRWPFQYNIGLKTNDKYVSLINYLPKNKIESTNVSQTLGYNIGGNFQSAPSLGGNGSFNYSKSISYTQQNYVSEVEQQNSKSVLWGVKANSFATESGQKSAFDSDLFVGYKPHSKDPRDYFVPDSELPPLVQSGFNPSFIATVSHEKGSSDTSEFEITYGRNMDVTHAIKRSTHYGNSYLDGHRVHNAFVNRNYTVKYEVNWKTHEIKVKGQN

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	158878
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Gamma-hemolysin component B
Molecular weight formula_weight	35310.1 kDa
Mutation mutation	C255R
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G

MGHHHHHHAMEGKITPVSVKKVDDKVTLYKTTATADSDKFKISQILTFNFIKDKSYDKDTLVLKATGNINSGFVKPNPNDYDFSKLYWGAKYNVSISSQSNDSVNVVDYAPKNQNEEFQVQNTLGYTFGGDISISNGLSGGLNGNTAFSETINYKQESYRTTLSRNTNYKNVGWGVEAHKIMNNGWGPYGRDSFHPTYGNELFLAGRQSSAYAGQNFIAQHQMPLLSRSNFNPEFLSVLSHRQDGAKKSKITVTYQREMDLYQIRWNGFYWAGANYKNFKTRTFKSTYEIDWENHKVKLLDTKETENNK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	158878
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1057

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4p1xa_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d4p1xb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

Domain ID domain_id	d4p1xc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d4p1xd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

Domain ID domain_id	d4p1xe_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d4p1xf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

Domain ID domain_id	d4p1xg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d4p1xh_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4p1xA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xD00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xE00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xF00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xG00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4p1xH00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

▶

Unit-cell length a length_a	193.310 Å
Unit-cell length b length_b	193.160 Å
Unit-cell length c length_c	116.380 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.295 Å
R factor r_factor	0.1826
R_work r_work	0.1820
R_free r_free	0.2229

Crystal structure of staphylococcal LUK prepore

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

Gamma-hemolysin component C

State in the Current Structure

Other States of the Same Protein in the Database

Gamma-hemolysin component B

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

4p1x__assembly_1__model_1

4p1x__assembly_1__model_1 | I(q)

4p1x__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of staphylococcal LUK prepore

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

Gamma-hemolysin component C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Gamma-hemolysin component 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4p1x__assembly_1__model_1

4p1x__assembly_1__model_1 | I(q)

4p1x__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)