SAXSdb — 7bwk

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

IcmO (DotL)

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48） PNPLA domain-containing protein × 1 （Q5ZW60）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48） PNPLA domain-containing protein × 1 （Q5ZW60）	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 656–783 Author chain F； PDBConstruct 1–128； UniProt 656–783

IcmS

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZYD0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48） PNPLA domain-containing protein × 1 （Q5ZW60）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48） PNPLA domain-containing protein × 1 （Q5ZW60）	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–114； UniProt 1–114 Author chain G； PDBConstruct 1–114； UniProt 1–114

IcmW

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZS31

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmS × 1 （Q5ZYD0） Hypothetical virulence protein × 1 （Q5ZY48） PNPLA domain-containing protein × 1 （Q5ZW60）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmS × 1 （Q5ZYD0） Hypothetical virulence protein × 1 （Q5ZY48） PNPLA domain-containing protein × 1 （Q5ZW60）	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–151； UniProt 1–151 Author chain H； PDBConstruct 1–151； UniProt 1–151

Hypothetical virulence protein

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZY48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） PNPLA domain-containing protein × 1 （Q5ZW60）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） PNPLA domain-containing protein × 1 （Q5ZW60）	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
Chains and sequence ranges	Author chain D； PDBConstruct 1–208； UniProt 1–208 Author chain I； PDBConstruct 1–208； UniProt 1–208

PNPLA domain-containing protein

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZW60

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） IcmS × 1 （Q5ZYD0） IcmW × 1 （Q5ZS31） Hypothetical virulence protein × 1 （Q5ZY48）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	IcmO (DotL) × 1 （Q5ZYC6） 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	Q5ZW60_LEGPH
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–130； UniProt 461–590 Author chain J； PDBConstruct 1–130； UniProt 461–590

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	7bwk
Deposition date deposition_date	2020-04-14
Structure title title	Structure of DotL(656-783)-IcmS-IcmW-LvgA-VpdB(461-590) derived from Legionella pneumophila
Keywords keywords	;Dot/Icm Type 4B Secretion System, effector recognition, Type 4B coupling protein complex-effector complex, DotL-IcmSW-LvgA, VpdB, 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.

7bwk__assembly_1__model_1

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

Download this curve (.dat)

7bwk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7bwk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.13 Å
Rg (electron density)	28.33 Å
Total Rg	29.06 Å
Atom count	5329
Residues	672
Excluded volume	95323 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7bwk__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7bwk__assembly_2__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	IcmO (DotL)
Molecular weight formula_weight	14216.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	10645

GQNEPEPVEDIVEEEVEGALTIFSKLRIDPNAPPILVADKEVFSEPLLPINETRNQMITIERLAGAKDKYAGTVANELIKDFQIATSYPPEERDVIDVQELTGIIRDLSAKISAEREKANKKAAEELT

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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	B,G

MERDISKCMAKIAASMNAKFYLNDRFVSFDEVFSETGLLPAIAKRADQLCSLCLGYGLGATYDESEGALLGIRVVFDEVTPNVLRLLCMTDVMNELIQGGPSRDYTPLDELMYD

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	IcmW
Molecular weight formula_weight	17349.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

MPDLSHEASAKYWFEYLDPMIYRVITFMESVENWTLDGNPELEEAMKQLGQELDDIEKIDLGLLAEEDKFIRIVGNIKSGRGLRLLQAIDTVHPGSASRVLIHAEETSLSSSDPAGFFLKRNIVFERLRLLSRVFCQYRLKLVLRALEGDE

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
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	23533.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

MADGDIEIKAGFVDTDLDDRKLTMIDDLNNPLAIVERVYLIWWHWADFHLHVISPHIDTITPAIVIEPELIPGSNDHEFVYSIHDSGSKLSTSKSQDMFSAGMSMCKLFYTIEKMVYILVERLKSGGVSMEAEVQIAFAGHEIAQRKAFESIINLPYNVVVTNFDPGIWGEKYLQNVKRLADKGYGYPPESPRKIYMHPVSSGTTARK

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	PNPLA domain-containing protein
Molecular weight formula_weight	14842.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J

NSSQQQEQLKEKTMLFKSRLQSFKQGEGVKPWSQHVENAIDRLMSLKGEITKAQVDLGRTWFDIKSENADPAVRLKKFNDAFLASPLAKPSSNQQEINFSKEIRKEIDLLKGLPGLNNTSSHCTEEFNEQ

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	188.992 Å
Unit-cell length b length_b	188.992 Å
Unit-cell length c length_c	170.252 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.801 Å
Low-resolution limit resolution_low	47.248 Å
R factor r_factor	0.2014
R_work r_work	0.1990
R_free r_free	0.2450

Structure of DotL(656-783)-IcmS-IcmW-LvgA-VpdB(461-590) derived from Legionella pneumophila

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

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

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

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

PNPLA domain-containing 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

7bwk__assembly_1__model_1

7bwk__assembly_1__model_1 | I(q)

7bwk__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 (5)

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

7. Citations (1)