5x90

Structure of DotL(656-783)-IcmS-IcmW-LvgA derived from Legionella pneumophila

Method: X-RAY DIFFRACTION

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

IcmS

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	IcmW × 1 （Q5ZS31） IcmO (DotL) × 1 （Q5ZYC6） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	IcmW × 1 （Q5ZS31） IcmO (DotL) × 1 （Q5ZYC6） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYD0_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–114； UniProt 1–114 Author chain E； PDBConstruct 1–114； UniProt 1–114

IcmW

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

UniProt Q5ZS31

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	IcmS × 1 （Q5ZYD0） IcmO (DotL) × 1 （Q5ZYC6） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	IcmS × 1 （Q5ZYD0） IcmO (DotL) × 1 （Q5ZYC6） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZS31_LEGPH
Isoform	—
PDB entities	2, 5
Chains and sequence ranges	Author chain F； PDBConstruct 1–149； UniProt 2–150 Author chain B； PDBConstruct 1–148； UniProt 2–149

IcmO (DotL)

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

UniProt Q5ZYC6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC6_LEGPH
Isoform	—
PDB entities	3, 6
Chains and sequence ranges	Author chain G； PDBConstruct 1–108； UniProt 672–779 Author chain C； PDBConstruct 1–107； UniProt 672–778

Hypothetical virulence protein

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

UniProt Q5ZY48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） IcmO (DotL) × 1 （Q5ZYC6）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） IcmO (DotL) × 1 （Q5ZYC6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZY48_LEGPH
Isoform	—
PDB entities	4, 7
Chains and sequence ranges	Author chain H； PDBConstruct 1–172； UniProt 22–193 Author chain D； PDBConstruct 1–171； UniProt 25–195

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	5x90
Deposition date deposition_date	2017-03-04
Structure title title	Structure of DotL(656-783)-IcmS-IcmW-LvgA derived from Legionella pneumophila
Keywords keywords	Type IV secretion system, Coupling protein complex, Effector translocation, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

5x90__assembly_1__model_1

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

Download this curve (.dat)

5x90__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5x90__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.14 Å
Rg (electron density)	23.93 Å
Total Rg	24.87 Å
Atom count	4084
Residues	537
Excluded volume	73113 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5x90__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5x90__assembly_2__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	IcmS
Molecular weight formula_weight	12682.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A
Atom count atom_count	8058

MERDISKCMAKIAASMNAKFYLNDRFVSFDEVFSETGLLPAIAKRADQLCSLCLGYGLGATYDESEGALLGIRVVFDEVTPNVLRLLCMTDVMNELIQGGPSRDYTPLDELMYD

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	IcmW
Molecular weight formula_weight	17089.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

PDLSHEASAKYWFEYLDPMIYRVITFMESVENWTLDGNPELEEAMKQLGQELDDIEKIDLGLLAEEDKFIRIVGNIKSGRGLRLLQAIDTVHPGSASRVLIHAEETSLSSSDPAGFFLKRNIVFERLRLLSRVFCQYRLKLVLRALEGD

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	IcmO (DotL)
Molecular weight formula_weight	11949.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

EGALTIFSKLRIDPNAPPILVADKEVFSEPLLPINETRNQMITIERLAGAKDKYAGTVANELIKDFQIATSYPPEERDVIDVQELTGIIRDLSAKISAEREKANKKAA

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Hypothetical virulence protein
Molecular weight formula_weight	19562.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

LTMIDDLNNPLAIVERVYLIWWHWADFHLHVISPHIDTITPAIVIEPELIPGSNDHEFVYSIHDSGSKLSTSKSQDMFSAGMSMCKLFYTIEKMVYILVERLKSGGVSMEAEVQIAFAGHEIAQRKAFESIINLPYNVVVTNFDPGIWGEKYLQNVKRLADKGYGYPPESPR

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	IcmW
Molecular weight formula_weight	16974.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PDLSHEASAKYWFEYLDPMIYRVITFMESVENWTLDGNPELEEAMKQLGQELDDIEKIDLGLLAEEDKFIRIVGNIKSGRGLRLLQAIDTVHPGSASRVLIHAEETSLSSSDPAGFFLKRNIVFERLRLLSRVFCQYRLKLVLRALEG

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	IcmO (DotL)
Molecular weight formula_weight	11878.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EGALTIFSKLRIDPNAPPILVADKEVFSEPLLPINETRNQMITIERLAGAKDKYAGTVANELIKDFQIATSYPPEERDVIDVQELTGIIRDLSAKISAEREKANKKA

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Hypothetical virulence protein
Molecular weight formula_weight	19459.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

IDDLNNPLAIVERVYLIWWHWADFHLHVISPHIDTITPAIVIEPELIPGSNDHEFVYSIHDSGSKLSTSKSQDMFSAGMSMCKLFYTIEKMVYILVERLKSGGVSMEAEVQIAFAGHEIAQRKAFESIINLPYNVVVTNFDPGIWGEKYLQNVKRLADKGYGYPPESPRKI

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	152.325 Å
Unit-cell length b length_b	152.325 Å
Unit-cell length c length_c	74.475 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	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	41.432 Å
R factor r_factor	0.2531
R_work r_work	0.2515
R_free r_free	0.2947

Structure of DotL(656-783)-IcmS-IcmW-LvgA derived from Legionella pneumophila

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

IcmS

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

IcmW

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

IcmO (DotL)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hypothetical virulence protein

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

5x90__assembly_1__model_1

5x90__assembly_1__model_1 | I(q)

5x90__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 (7)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

7. Citations (1)