SAXSdb — 9ngy

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

IcmX (IcmY)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	DotA × 5 （Q5ZS33） IcmE (DotG) × 5 （Q5ZYC1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZS30_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AP1； PDBConstruct 1–466； UniProt 1–466 Author chain BP1； PDBConstruct 1–466； UniProt 1–466 Author chain CP1； PDBConstruct 1–466； UniProt 1–466 Author chain DP1； PDBConstruct 1–466； UniProt 1–466 Author chain EP1； PDBConstruct 1–466； UniProt 1–466

DotA

OrganismNot specified

UniProt Q5ZS33

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	IcmX (IcmY) × 5 （Q5ZS30） IcmE (DotG) × 5 （Q5ZYC1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZS33_LEGPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain FP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain GP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain HP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain IP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain JP1； PDBConstruct 1–1048； UniProt 1–1048

IcmE (DotG)

OrganismNot specified

UniProt Q5ZYC1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	IcmX (IcmY) × 5 （Q5ZS30） DotA × 5 （Q5ZS33）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC1_LEGPH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain KP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain LP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain MP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain NP1； PDBConstruct 1–1048； UniProt 1–1048 Author chain OP1； PDBConstruct 1–1048； UniProt 1–1048

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	9ngy
Deposition date deposition_date	2025-02-22
Structure title title	In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine
Keywords keywords	Type IVB Dot/Icm Secretion Machine, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

9ngy__assembly_1__model_1

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

Download this curve (.dat)

9ngy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ngy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	67.85 Å
Rg (electron density)	68.08 Å
Total Rg	68.09 Å
Atom count	50535
Residues	6585
Excluded volume	907500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ngy__assembly_1__model_1`	15-meric （15）	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	IcmX (IcmY)
Molecular weight formula_weight	50712.4 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AP1,BP1,CP1,DP1,EP1
Atom count atom_count	50535

MKVLPKLALANLVCFTTLSVFAQPADPSGQQTSTNTSNLVTYLTNLGKYLGYDITQSSKAPNPPYSQLFNSNVVQLVQNYAYNTFLGAIPVDAMSQSLMNFVTDKVQGNSLINNLANTTFKYQNFSAPSSGADGKITANGLIDQSTASAQTPTTPGIFSAPQITTSGTYLNDPVSQAVFNILGTPDYSFCMDNEQKNWLPNCNLMYQNLVMQNVIGTLPPAQTSGSTPAFYSYKYNQPLISQLNSNSLIAPLLMDTSASQSGQDSGLTAKSQAQQALNFIRYASAQVTPPSLPKLSAYSELWNQATAKPNSAGYNEVQQKQAAATLSSYFNNLRVYAAQTSVGVSNLYYILSKRLPQNMSADQSNANITSQALNEFNMATRRLFDPTASNTPGQPNQQWIKQINDASPATVQKEIAILLAEINYQMYLDRQIQERILLTNSIMLLQNLKAAQPTADFSSQGSPSEQ

Entity 2 Entity 2 polymer

Description description	DotA
Molecular weight formula_weight	113235.6 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	FP1,GP1,HP1,IP1,JP1

MNKLAITVLLCFFPALALAENGALSFAPPASDLSVVFLGNLFGVVDGVLHGTGSQIMGNMFGVFNSAVLALGGIIIMYTLMVSTMNTAHEGQMLGQKWSSIWIPLRSTFGLALLIPKASGYCMMQVFFMWVIVQGVGAADKIWEAALSYLNRGGVIIQAQADPTKSLQAAGSSSSGVAKGALTILGGQICMLGLQKQLQAQRDLYLSQSKSPPCGGNPTPEMNTFCRTAIPDFISTVNFVKKQNDDTPKDLTANQPASFELDMPNFDKSSPFYFLNGICGTVKWNNISALNSTNQSDNKGLVTVGGAGSNSSMGANSLNITSSQLQTARLSRAIAIQQMYVTLSTVAQVMVNNDPAFSTTTSTGNSKNDFSAIAKQQFGVPYKSSGEVCTEYQQVCQTWGSVPSSTGSTTGVLFNGTEFLGAINDYNGIMMPTLNLIRQATSKEFDKKSRDFIAEANAKGWIMAGSYFFDLVKLNGSATEFADQFDTGTGLDKSSFDPTQLTKPFGKTCQDPYSLLCTWFQNKSDKLIQIQSLIDGVPALGQDGVKQPDLSDNPQRQSVSGPLSSTVYGFVNNSMMVQLPGQPGIKPLTFANLINFKVDTSLYYMKHQDFDCGRVKILFFSFCLGRMMGDLFYNYVFRYVYNFFLAIFGEMINSIVMAFLMIPLQGMKDIFIVGVQTLTQPGINPIVALANMGTMYINFSGTLWLTLLNMAVVSSLIPLFGIFIFALIMMAMPLLMAWIGTMVSIGFVTAYYIPVLPYMIFTFGSFAWLIAVIEAMVAAPIVALGVTHPEGNEAFGKGEFAIMILVNVFLRPSLMIIGYIAAIALSYVGVWILNAGFDHAISYIQSDQGIETWEKGTSSNDAKRFFQSAGNWTGAKMDTSQWDNFKDKLTGDYQSTALEGGYTGWAGVYAFFFSILIYTSMYLIIVQKAFTLIAHLPDKVLRWIGGSPESFGQETMQWGEEAKGRVEKAGEATYGAEKAIGDKLGAKGQEMLGKLGPQAKKISENAGDVSGKGKNSGGSQTGPSSKPDTGQQLGGSDSGTPTSTPPPE

Entity 3 Entity 3 polymer

Description description	IcmE (DotG)
Molecular weight formula_weight	107911.9 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	KP1,LP1,MP1,NP1,OP1

MASKKENLKSLFSNTRTRVIIIFTAALLIIAVVIGFFKIRGATTGSIAAAEVSTVPGGIQSIPGVLDPTAQYAKLQEEQNITQAQVAEKTGGSAIPTIIRTQALGEGVGVIGSQSGVGFAALAQEELGGPQRSLWIQELQDGSCSKSVITKVVNQGAQLTDLKAACSCVQLKDSGYGLQELEQVCECKELKSAGYNARQLKEAGYSAGRLRNCGFDACELRNAGFTAQEMKDGGFSDGELKGAGFSDAEIAKASGLPDGITADDVRKAGCGAAALAKLRQAGVSASAIRKISGCTAEQLKAAGYTAKELKDAGFSAADLRRAGFSAAELKDAGFTARDLLNAGFTPADLAKAGFSDAQIKAAQAELPPGITPQDVKNAGCDVEALKKEREAGVSAALIRQYAGCSAQALKAAGFTDADLANAGFTPAQISAATPLSDAEIKAAGCDPDKLKKLFSAGVSAKRIKELNGCSAEALKAAGYDAQSLLAAGFTPQELLAAGFTPKQLEDAGLNPVSIIADGRVADCSVESLKKARAAGVSALTIKQTLGCSAAALKAAGYTAKELKDAGFTAAELKAAGFSAKELKDAGFTAKELRDAGFSAQELKDVGFSAKDLKDAGFSAAELKAAGFTAAQLKAAGFSAKDLKDAGFSAAELKAAGFSAKELKDAGFSASDLKNAGFSAKELKDAGFSASDLKSAGFSASELKNAGYSADELKKAGYTSAELRNAGFSPQESAVAGLQGPDLQQLDSSITGIPSIPGATPRPTTSDAASSAEQLQAILQKQNEQLAEQKYQQEIQQRTSDMLTAATQLVQDWKQVETQVYTEGTEETKTSGGESAVPGTGTGTGSNNQPVDQGAVSAQNQAIIKTGDIMFAVLDTSVNSDEPGPILATIVTGKLKGSKLIGSFNLPSNADKMVITFNTMSIPGAEKTISISAYAIDPNTARTALASRTNHHYLMRYGSLFASSFLQGFGNAFQSANTTITIGGTGGGNNITVANGVGRSTLENAVIGLATVGKAWSQQAQQLFNTPTTVEVYSGTGLGILFTQDVTTI

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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	triclinic

Resolution resolution	3.63 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	37503

In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine

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

IcmX (IcmY)

State in the Current Structure

Other States of the Same Protein in the Database

DotA

State in the Current Structure

Other States of the Same Protein in the Database

IcmE (DotG)

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

9ngy__assembly_1__model_1

9ngy__assembly_1__model_1 | I(q)

9ngy__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Citations (2)

In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine

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

IcmX (IcmY)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DotA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

IcmE (DotG)

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

9ngy__assembly_1__model_1

9ngy__assembly_1__model_1 | I(q)

9ngy__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Citations (2)