SAXSdb — 7ovb

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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	IcmP (DotM) × 1 （Q5ZYC7） IcmJ (DotN) × 1 （Q5ZYB7） DotZ × 1 （Q5ZV91） DotY × 1 （Q5ZYR7） ZINC ION × 1	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 1–783； UniProt 1–783

IcmP (DotM)

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZYC7

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） IcmJ (DotN) × 1 （Q5ZYB7） DotZ × 1 （Q5ZV91） DotY × 1 （Q5ZYR7） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC7_LEGPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–380； UniProt 1–380

IcmJ (DotN)

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZYB7

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） IcmP (DotM) × 1 （Q5ZYC7） DotZ × 1 （Q5ZV91） DotY × 1 （Q5ZYR7） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYB7_LEGPH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–208； UniProt 7–214

DotZ

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZV91

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） IcmP (DotM) × 1 （Q5ZYC7） IcmJ (DotN) × 1 （Q5ZYB7） DotY × 1 （Q5ZYR7） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZV91_LEGPH
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–294； UniProt 1–294

DotY

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZYR7

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） IcmP (DotM) × 1 （Q5ZYC7） IcmJ (DotN) × 1 （Q5ZYB7） DotZ × 1 （Q5ZV91） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYR7_LEGPH
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–230； UniProt 1–230

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	7ovb
Deposition date deposition_date	2021-06-14
Structure title title	L. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains
Keywords keywords	;Type IV Coupling Complex, T4CC, Type IV Secretion System, T4SS, Membrane protein complex, Membrane complex, DotY, DotZ, DotL, DotM, DotN, IcmSW, Legionella, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

7ovb__assembly_1__model_1

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

Download this curve (.dat)

7ovb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ovb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.81 Å
Rg (electron density)	40.55 Å
Total Rg	40.71 Å
Atom count	10854
Residues	1405
Excluded volume	193630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ovb__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	IcmO (DotL)
Molecular weight formula_weight	87601.0 kDa
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	10854

MMRGIDSRHELDPTLLLRDTRTFTQRLADFFADPTNISIVLISLAAVSYYFSEAATFLLIMGGIFFLYSYTRKQKLPFRLPQISRAKDYNDLKPGINKPNIARGITFFGNDRKTGEELWFANDDMRTHALIFGSTGSGKTETLVSLSYNALVQGSGFIYVDGKGDNSLYAKVFSMVRSMGREDDLLLINFMTGARDIVGPQEKRLSNTLNPFCQGSSSMLTQLVVSLMGSSGQSSDGDMWKGRAIAFVEALMRLLVYMRDEGAILLDANTIRNYFDLQRLESIVIDKVFPRDDQESVNIETIPKLVTDPLRNYLNTLPGYNKEKKGKQVSQVLEQHGFITMQLVRSFSSLADTYGHIIRTNLAEVDFKDVVLNRRILVVLLPALEKSPDELSNLGKIIVSSLKAMMAAGLGEEVEGDYRDVILRKPTNAPTPYMCILDEYGYYAVQGFAVVPAQARSLGFSAIFAGQDLPAFQKASKEEAASIGANTNIKICMKLEDPTETWDFFTKTAGEAYVTKVDSFQTKETSIANSYMDTKSSSFEKRARVDLLDLKEQTEGEAHIFFKSKIVRARMFYANPKPVKQLKINQFLKVEPPPDDYLMKLQKQLASFQSILESGDLSINKAVENEEITLISKALKESTIVEPIERGVAALIAFHGQNEPEPVEDIVEEEVEGALTIFSKLRIDPNAPPILVADKEVFSEPLLPINETRNQMITIERLAGAKDKYAGTVANELIKDFQIATSYPPEERDVIDVQELTGIIRDLSAKISAEREKANKKAAEELT

Source Source

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

Entity 2 Entity 2 polymer

Description description	IcmP (DotM)
Molecular weight formula_weight	43858.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MYIEMAQQQQQSGSDNSMAPVWIVILLFITAYFVWALAHQYIVSFVFTINIWQARLVNLFLNNQLLANQIYLMQTLDPNTVNWDQMVTVMRAVGDYMRYPVICILVVLAFVLYNSNVTLKYRKTYDMKSLRAQEQFNWPAIMPIVKEDLVSQDVNKGPWAMALTPMEFARKYNLLRKDDALLDNPVPGEEMTAGIRRGDAKRVFTMQLGPYWDGFERCSPQAYALSAVFMARMNRDRDAANNILKVLDKTFVDGKPDFSVARPVMKKYQNSELVQEVVAKHAYVLTVIASLLEAAREDGVVPSSEFLWLKPVDRRLWYMLNCVGRQTPYSEVAGPFAHWKAEKEMGRRSLVPMIDEAIRALEIAVKEVRLTPRQMEELEP

Source Source

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

Entity 3 Entity 3 polymer

Description description	IcmJ (DotN)
Molecular weight formula_weight	23763.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MADNQQRCELKLIASPGSWRLYSARKIDERFKSYEQKIFQRDRYTCQFCGFQARLYQDIVNLDGDYTNNRLSNLVTACCFCAQCFFVESVGVGGYGGGTLIYLPELTQAELNSLCHVLFCAITNDTGYKSSAQNIYRSFKFRSQIVEEKFGEGTSDPAIFGQLMIDSGVNSEEIREKLFKNIRLLPSRAKFRKQIEKWAASALEEIAD

Source Source

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

Entity 4 Entity 4 polymer

Description description	DotZ
Molecular weight formula_weight	33887.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MDEIKKDDELSQWLSTYGTITAERILGRYNISLPQDEILEAINIPSSFYRHLLQIPLKNVLNGIVIQQASDYHVYAQKLLIDYLLSGESSKEPDSQGAGTRESLEDERQRLVQLGDEFHKLELEQDNLIASSQASLMKISIDWNTKLETTLSKLNSLYKNTNSKIKKNAIRKALIKAFIHCDLVKDQSQKNKYQLIDKLNQTLAVSVGAELKESILTNLSELFQILEALNTKLDEFTDRTNHLSQQAKSFRTQFYEVILRIIELIKLLPEYKIDPAQDAINREPLYFDRTIGER

Source Source

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

Entity 5 Entity 5 polymer

Description description	DotY
Molecular weight formula_weight	25551.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MPKYTLPTRDALLKAMQVGETSIEAAEYMATRFEQILTKAKLLPECNDMLEKIKEYAQFVKFKLLSSAQVWSGQERPTSDYQNTQENKAEFLASHLEGLPSGLKLEVAIGDDAKILRGFSSNGKMVEGDQLKTMDGLLEGWLAKNSLAISGGAVVKIDNTGNQTKVDPQEIRQLINDSEKGVAKYFADKGVGMEVAQRTYQEPKALETKREEIRQEIESGAEAPTTQSIR

Source Source

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

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.61 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	183397

L. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains

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

IcmP (DotM)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

IcmJ (DotN)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DotZ

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DotY

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

7ovb__assembly_1__model_1

7ovb__assembly_1__model_1 | I(q)

7ovb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

7. Citations (1)