9ngv

In situ cryo-EM structure of periplasmic ring (PR) of the Legionella Dot/Icm T4SS machine.

Method: ELECTRON MICROSCOPY

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

IcmG (DotF)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 126	unknown peptide A × 18 unknown peptide B × 18 unknown peptide C × 18 unknown peptide D × 18 IcmE (DotG) × 18 （Q5ZYC1） IcmK (DotH) × 18 （Q5ZYC2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC0_LEGPH
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain Ae； PDBConstruct 1–269； UniProt 1–269 Author chain Al； PDBConstruct 1–269； UniProt 1–269 Author chain As； PDBConstruct 1–269； UniProt 1–269 Author chain Az； PDBConstruct 1–269； UniProt 1–269 Author chain Bg； PDBConstruct 1–269； UniProt 1–269 Author chain Bn； PDBConstruct 1–269； UniProt 1–269 Author chain Bu； PDBConstruct 1–269； UniProt 1–269 Author chain Cb； PDBConstruct 1–269； UniProt 1–269 Author chain Ci； PDBConstruct 1–269； UniProt 1–269 Author chain Cp； PDBConstruct 1–269； UniProt 1–269 Author chain Cw； PDBConstruct 1–269； UniProt 1–269 Author chain Dd； PDBConstruct 1–269； UniProt 1–269 Author chain Dk； PDBConstruct 1–269； UniProt 1–269 Author chain Dr； PDBConstruct 1–269； UniProt 1–269 Author chain Dy； PDBConstruct 1–269； UniProt 1–269 Author chain Ef； PDBConstruct 1–269； UniProt 1–269 Author chain Em； PDBConstruct 1–269； UniProt 1–269 Author chain Et； PDBConstruct 1–269； UniProt 1–269

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 126	unknown peptide A × 18 unknown peptide B × 18 unknown peptide C × 18 unknown peptide D × 18 IcmG (DotF) × 18 （Q5ZYC0） IcmK (DotH) × 18 （Q5ZYC2）	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	6
Chains and sequence ranges	Author chain Af； PDBConstruct 1–1048； UniProt 1–1048 Author chain Am； PDBConstruct 1–1048； UniProt 1–1048 Author chain At； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ba； PDBConstruct 1–1048； UniProt 1–1048 Author chain Bh； PDBConstruct 1–1048； UniProt 1–1048 Author chain Bo； PDBConstruct 1–1048； UniProt 1–1048 Author chain Bv； PDBConstruct 1–1048； UniProt 1–1048 Author chain Cc； PDBConstruct 1–1048； UniProt 1–1048 Author chain Cj； PDBConstruct 1–1048； UniProt 1–1048 Author chain Cq； PDBConstruct 1–1048； UniProt 1–1048 Author chain Cx； PDBConstruct 1–1048； UniProt 1–1048 Author chain De； PDBConstruct 1–1048； UniProt 1–1048 Author chain Dl； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ds； PDBConstruct 1–1048； UniProt 1–1048 Author chain Dz； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eg； PDBConstruct 1–1048； UniProt 1–1048 Author chain En； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eu； PDBConstruct 1–1048； UniProt 1–1048

IcmK (DotH)

OrganismNot specified

UniProt Q5ZYC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 126	unknown peptide A × 18 unknown peptide B × 18 unknown peptide C × 18 unknown peptide D × 18 IcmG (DotF) × 18 （Q5ZYC0） IcmE (DotG) × 18 （Q5ZYC1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZYC2_LEGPH
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain Ag； PDBConstruct 1–361； UniProt 1–361 Author chain An； PDBConstruct 1–361； UniProt 1–361 Author chain Au； PDBConstruct 1–361； UniProt 1–361 Author chain Bb； PDBConstruct 1–361； UniProt 1–361 Author chain Bi； PDBConstruct 1–361； UniProt 1–361 Author chain Bp； PDBConstruct 1–361； UniProt 1–361 Author chain Bw； PDBConstruct 1–361； UniProt 1–361 Author chain Cd； PDBConstruct 1–361； UniProt 1–361 Author chain Ck； PDBConstruct 1–361； UniProt 1–361 Author chain Cr； PDBConstruct 1–361； UniProt 1–361 Author chain Cy； PDBConstruct 1–361； UniProt 1–361 Author chain Df； PDBConstruct 1–361； UniProt 1–361 Author chain Dm； PDBConstruct 1–361； UniProt 1–361 Author chain Dt； PDBConstruct 1–361； UniProt 1–361 Author chain Ea； PDBConstruct 1–361； UniProt 1–361 Author chain Eh； PDBConstruct 1–361； UniProt 1–361 Author chain Eo； PDBConstruct 1–361； UniProt 1–361 Author chain Ev； PDBConstruct 1–361； UniProt 1–361

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	9ngv
Deposition date deposition_date	2025-02-22
Structure title title	In situ cryo-EM structure of periplasmic ring (PR) 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.

9ngv__assembly_1__model_1

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

Download this curve (.dat)

9ngv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ngv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	74.12 Å
Rg (electron density)	73.55 Å
Total Rg	73.81 Å
Atom count	42066
Residues	5454
Excluded volume	751670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ngv__assembly_1__model_1`	126-meric （126）	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	unknown peptide A
Molecular weight formula_weight	1679.8 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Aa,Ah,Ao,Av,Bc,Bj,Bq,Bx,Ce,Cl,Cs,Cz,Dg,Dn,Du,Eb,Ei,Ep
Atom count atom_count	42066

CTDAALAALEYHKSNA

Entity 2 Entity 2 polymer

Description description	unknown peptide B
Molecular weight formula_weight	910.1 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ab,Ai,Ap,Aw,Bd,Bk,Br,By,Cf,Cm,Ct,Da,Dh,Do,Dv,Ec,Ej,Eq

CVSMIGGSR

Entity 3 Entity 3 polymer

Description description	unknown peptide C
Molecular weight formula_weight	1776.0 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ac,Aj,Aq,Ax,Be,Bl,Bs,Bz,Cg,Cn,Cu,Db,Di,Dp,Dw,Ed,Ek,Er

RVSIGGTVYTAKKYDD

Entity 4 Entity 4 polymer

Description description	unknown peptide D
Molecular weight formula_weight	505.5 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ad,Ak,Ar,Ay,Bf,Bm,Bt,Ca,Ch,Co,Cv,Dc,Dj,Dq,Dx,Ee,El,Es

PFGAD

Entity 5 Entity 5 polymer

Description description	IcmG (DotF)
Molecular weight formula_weight	29730.0 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ae,Al,As,Az,Bg,Bn,Bu,Cb,Ci,Cp,Cw,Dd,Dk,Dr,Dy,Ef,Em,Et

MMAEHDQNNDEYKFAELDSYDMDQAGESDLDSEASYQSGKEGLTKKKDIKRNALIAIGAVVFIMVMYKIIGWMFFSDKSSQVTSKPAIPPVTQVATPQPVQTIPTTTPIQQVQPTTIIEDDPDLKKKVSAIEMTQQSLRSEVNALSEQINAVNNNIKNLNAQIVNLNQIIGNMSNQIARQSEVINVLMARTTPKKVVKVSRPIVQARIIYYIQAVIPGRAWLIGSNGSTLTVREGSKIPGYGMVKLIDSLQGRILTSSGQVIKFSQEDS

Entity 6 Entity 6 polymer

Description description	IcmE (DotG)
Molecular weight formula_weight	107911.9 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Af,Am,At,Ba,Bh,Bo,Bv,Cc,Cj,Cq,Cx,De,Dl,Ds,Dz,Eg,En,Eu

MASKKENLKSLFSNTRTRVIIIFTAALLIIAVVIGFFKIRGATTGSIAAAEVSTVPGGIQSIPGVLDPTAQYAKLQEEQNITQAQVAEKTGGSAIPTIIRTQALGEGVGVIGSQSGVGFAALAQEELGGPQRSLWIQELQDGSCSKSVITKVVNQGAQLTDLKAACSCVQLKDSGYGLQELEQVCECKELKSAGYNARQLKEAGYSAGRLRNCGFDACELRNAGFTAQEMKDGGFSDGELKGAGFSDAEIAKASGLPDGITADDVRKAGCGAAALAKLRQAGVSASAIRKISGCTAEQLKAAGYTAKELKDAGFSAADLRRAGFSAAELKDAGFTARDLLNAGFTPADLAKAGFSDAQIKAAQAELPPGITPQDVKNAGCDVEALKKEREAGVSAALIRQYAGCSAQALKAAGFTDADLANAGFTPAQISAATPLSDAEIKAAGCDPDKLKKLFSAGVSAKRIKELNGCSAEALKAAGYDAQSLLAAGFTPQELLAAGFTPKQLEDAGLNPVSIIADGRVADCSVESLKKARAAGVSALTIKQTLGCSAAALKAAGYTAKELKDAGFTAAELKAAGFSAKELKDAGFTAKELRDAGFSAQELKDVGFSAKDLKDAGFSAAELKAAGFTAAQLKAAGFSAKDLKDAGFSAAELKAAGFSAKELKDAGFSASDLKNAGFSAKELKDAGFSASDLKSAGFSASELKNAGYSADELKKAGYTSAELRNAGFSPQESAVAGLQGPDLQQLDSSITGIPSIPGATPRPTTSDAASSAEQLQAILQKQNEQLAEQKYQQEIQQRTSDMLTAATQLVQDWKQVETQVYTEGTEETKTSGGESAVPGTGTGTGSNNQPVDQGAVSAQNQAIIKTGDIMFAVLDTSVNSDEPGPILATIVTGKLKGSKLIGSFNLPSNADKMVITFNTMSIPGAEKTISISAYAIDPNTARTALASRTNHHYLMRYGSLFASSFLQGFGNAFQSANTTITIGGTGGGNNITVANGVGRSTLENAVIGLATVGKAWSQQAQQLFNTPTTVEVYSGTGLGILFTQDVTTI

Entity 7 Entity 7 polymer

Description description	IcmK (DotH)
Molecular weight formula_weight	38958.9 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ag,An,Au,Bb,Bi,Bp,Bw,Cd,Ck,Cr,Cy,Df,Dm,Dt,Ea,Eh,Eo,Ev

MMKKYDQLCKYCLVIGLTFSMSCSIYAADQSDDAQQALQQLRMLQQKLSQNPSPDAQSGAGDGGDNAASDSTQQPNQSGQANAPAANQTATAGGDGQIISQDDAEVIDKKAFKDMTRNLYPLNPEQVVKLKQIYETSEYAKAATPGTPPKPTATSQFVNLSPGSTPPVIRLSQGFVSSLVFLDSTGAPWPIAAYDLGDPSSFNIQWDKTSNTLMIQATKLYNYGNLAVRLRGLNTPVMLTLIPGQKAVDYRVDLRVQGYGPNAKSMPTEEGIPPSANDLLLHVLEGVPPPGSRRLVVSGGDARAWLSNEKMYVRTNLTILSPGWLASMTSADGTHAYEMQKSPVLLVSWHGKVMQLKVEGL

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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	3.04 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	76406

In situ cryo-EM structure of periplasmic ring (PR) of the Legionella Dot/Icm T4SS machine.

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

IcmG (DotF)

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

IcmK (DotH)

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

9ngv__assembly_1__model_1

9ngv__assembly_1__model_1 | I(q)

9ngv__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

7. Citations (2)

In situ cryo-EM structure of periplasmic ring (PR) of the Legionella Dot/Icm T4SS machine.

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

IcmG (DotF)

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

IcmK (DotH)

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

9ngv__assembly_1__model_1

9ngv__assembly_1__model_1 | I(q)

9ngv__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

7. Citations (2)