9nh0

In situ cryo-EM structure of PR and DotA-IcmX of the Legionella Dot/Icm T4SS machine at C1 symmetry

Method: ELECTRON MICROSCOPY

▼

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 141	unknown peptide E × 18 unknown peptide F × 18 unknown peptide G × 18 unknown peptide H × 18 IcmK (DotH) × 18 （Q5ZYC2） IcmE (DotG) × 23 （Q5ZYC1） 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	Q5ZYC0_LEGPH
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain Ae； PDBConstruct 1–269； UniProt 1–269 Author chain Ak； PDBConstruct 1–269； UniProt 1–269 Author chain Aq； PDBConstruct 1–269； UniProt 1–269 Author chain Aw； PDBConstruct 1–269； UniProt 1–269 Author chain Bc； PDBConstruct 1–269； UniProt 1–269 Author chain Bi； PDBConstruct 1–269； UniProt 1–269 Author chain Bo； PDBConstruct 1–269； UniProt 1–269 Author chain Bu； PDBConstruct 1–269； UniProt 1–269 Author chain Ca； PDBConstruct 1–269； UniProt 1–269 Author chain Cg； PDBConstruct 1–269； UniProt 1–269 Author chain Cm； PDBConstruct 1–269； UniProt 1–269 Author chain Cs； PDBConstruct 1–269； UniProt 1–269 Author chain Cy； PDBConstruct 1–269； UniProt 1–269 Author chain De； PDBConstruct 1–269； UniProt 1–269 Author chain Dk； PDBConstruct 1–269； UniProt 1–269 Author chain Dq； PDBConstruct 1–269； UniProt 1–269 Author chain Dw； PDBConstruct 1–269； UniProt 1–269 Author chain Ec； PDBConstruct 1–269； UniProt 1–269

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 141	unknown peptide E × 18 unknown peptide F × 18 unknown peptide G × 18 unknown peptide H × 18 IcmG (DotF) × 18 （Q5ZYC0） IcmE (DotG) × 23 （Q5ZYC1） 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	Q5ZYC2_LEGPH
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain Af； PDBConstruct 1–361； UniProt 1–361 Author chain Al； PDBConstruct 1–361； UniProt 1–361 Author chain Ar； PDBConstruct 1–361； UniProt 1–361 Author chain Ax； PDBConstruct 1–361； UniProt 1–361 Author chain Bd； PDBConstruct 1–361； UniProt 1–361 Author chain Bj； PDBConstruct 1–361； UniProt 1–361 Author chain Bp； PDBConstruct 1–361； UniProt 1–361 Author chain Bv； PDBConstruct 1–361； UniProt 1–361 Author chain Cb； PDBConstruct 1–361； UniProt 1–361 Author chain Ch； PDBConstruct 1–361； UniProt 1–361 Author chain Cn； PDBConstruct 1–361； UniProt 1–361 Author chain Ct； PDBConstruct 1–361； UniProt 1–361 Author chain Cz； PDBConstruct 1–361； UniProt 1–361 Author chain Df； PDBConstruct 1–361； UniProt 1–361 Author chain Dl； PDBConstruct 1–361； UniProt 1–361 Author chain Dr； PDBConstruct 1–361； UniProt 1–361 Author chain Dx； PDBConstruct 1–361； UniProt 1–361 Author chain Ed； PDBConstruct 1–361； UniProt 1–361

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 141	unknown peptide E × 18 unknown peptide F × 18 unknown peptide G × 18 unknown peptide H × 18 IcmG (DotF) × 18 （Q5ZYC0） IcmK (DotH) × 18 （Q5ZYC2） 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	7
Chains and sequence ranges	Author chain Ee； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ef； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eg； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eh； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ei； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ej； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ek； PDBConstruct 1–1048； UniProt 1–1048 Author chain El； PDBConstruct 1–1048； UniProt 1–1048 Author chain Em； PDBConstruct 1–1048； UniProt 1–1048 Author chain En； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eo； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ep； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eq； PDBConstruct 1–1048； UniProt 1–1048 Author chain Er； PDBConstruct 1–1048； UniProt 1–1048 Author chain Es； PDBConstruct 1–1048； UniProt 1–1048 Author chain Et； PDBConstruct 1–1048； UniProt 1–1048 Author chain Eu； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ev； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fg； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fh； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fi； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fj； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fk； PDBConstruct 1–1048； UniProt 1–1048

IcmX (IcmY)

OrganismNot specified

UniProt Q5ZS30

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 141	unknown peptide E × 18 unknown peptide F × 18 unknown peptide G × 18 unknown peptide H × 18 IcmG (DotF) × 18 （Q5ZYC0） IcmK (DotH) × 18 （Q5ZYC2） IcmE (DotG) × 23 （Q5ZYC1） DotA × 5 （Q5ZS33）	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	8
Chains and sequence ranges	Author chain Ew； PDBConstruct 1–466； UniProt 1–466 Author chain Ex； PDBConstruct 1–466； UniProt 1–466 Author chain Ey； PDBConstruct 1–466； UniProt 1–466 Author chain Ez； PDBConstruct 1–466； UniProt 1–466 Author chain Fa； 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 141	unknown peptide E × 18 unknown peptide F × 18 unknown peptide G × 18 unknown peptide H × 18 IcmG (DotF) × 18 （Q5ZYC0） IcmK (DotH) × 18 （Q5ZYC2） IcmE (DotG) × 23 （Q5ZYC1） IcmX (IcmY) × 5 （Q5ZS30）	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	9
Chains and sequence ranges	Author chain Fb； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fc； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fd； PDBConstruct 1–1048； UniProt 1–1048 Author chain Fe； PDBConstruct 1–1048； UniProt 1–1048 Author chain Ff； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9nh0
Deposition date deposition_date	2025-02-23
Structure title title	In situ cryo-EM structure of PR and DotA-IcmX of the Legionella Dot/Icm T4SS machine at C1 symmetry
Keywords keywords	Type IVB Dot/Icm Secretion Machine, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9nh0__assembly_1__model_1

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

Download this curve (.dat)

9nh0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9nh0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	74.31 Å
Rg (electron density)	74.25 Å
Total Rg	74.40 Å
Atom count	94015
Residues	12213
Excluded volume	1684000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9nh0__assembly_1__model_1`	141-meric （141）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	unknown peptide E
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,Ag,Am,As,Ay,Be,Bk,Bq,Bw,Cc,Ci,Co,Cu,Da,Dg,Dm,Ds,Dy
Atom count atom_count	94015

CTDAALAALEYHKSNA

Entity 2 Entity 2 polymer

Description description	unknown peptide F
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,Ah,An,At,Az,Bf,Bl,Br,Bx,Cd,Cj,Cp,Cv,Db,Dh,Dn,Dt,Dz

CVSMIGGSR

Entity 3 Entity 3 polymer

Description description	unknown peptide G
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,Ai,Ao,Au,Ba,Bg,Bm,Bs,By,Ce,Ck,Cq,Cw,Dc,Di,Do,Du,Ea

RVSIGGTVYTAKKYDD

Entity 4 Entity 4 polymer

Description description	unknown peptide H
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,Aj,Ap,Av,Bb,Bh,Bn,Bt,Bz,Cf,Cl,Cr,Cx,Dd,Dj,Dp,Dv,Eb

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,Ak,Aq,Aw,Bc,Bi,Bo,Bu,Ca,Cg,Cm,Cs,Cy,De,Dk,Dq,Dw,Ec

MMAEHDQNNDEYKFAELDSYDMDQAGESDLDSEASYQSGKEGLTKKKDIKRNALIAIGAVVFIMVMYKIIGWMFFSDKSSQVTSKPAIPPVTQVATPQPVQTIPTTTPIQQVQPTTIIEDDPDLKKKVSAIEMTQQSLRSEVNALSEQINAVNNNIKNLNAQIVNLNQIIGNMSNQIARQSEVINVLMARTTPKKVVKVSRPIVQARIIYYIQAVIPGRAWLIGSNGSTLTVREGSKIPGYGMVKLIDSLQGRILTSSGQVIKFSQEDS

Entity 6 Entity 6 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	Af,Al,Ar,Ax,Bd,Bj,Bp,Bv,Cb,Ch,Cn,Ct,Cz,Df,Dl,Dr,Dx,Ed

MMKKYDQLCKYCLVIGLTFSMSCSIYAADQSDDAQQALQQLRMLQQKLSQNPSPDAQSGAGDGGDNAASDSTQQPNQSGQANAPAANQTATAGGDGQIISQDDAEVIDKKAFKDMTRNLYPLNPEQVVKLKQIYETSEYAKAATPGTPPKPTATSQFVNLSPGSTPPVIRLSQGFVSSLVFLDSTGAPWPIAAYDLGDPSSFNIQWDKTSNTLMIQATKLYNYGNLAVRLRGLNTPVMLTLIPGQKAVDYRVDLRVQGYGPNAKSMPTEEGIPPSANDLLLHVLEGVPPPGSRRLVVSGGDARAWLSNEKMYVRTNLTILSPGWLASMTSADGTHAYEMQKSPVLLVSWHGKVMQLKVEGL

Entity 7 Entity 7 polymer

Description description	IcmE (DotG)
Molecular weight formula_weight	107911.9 kDa
Source method src_method	nat
Copy count entity_count	23

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ee,Ef,Eg,Eh,Ei,Ej,Ek,El,Em,En,Eo,Ep,Eq,Er,Es,Et,Eu,Ev,Fg,Fh,Fi,Fj,Fk

MASKKENLKSLFSNTRTRVIIIFTAALLIIAVVIGFFKIRGATTGSIAAAEVSTVPGGIQSIPGVLDPTAQYAKLQEEQNITQAQVAEKTGGSAIPTIIRTQALGEGVGVIGSQSGVGFAALAQEELGGPQRSLWIQELQDGSCSKSVITKVVNQGAQLTDLKAACSCVQLKDSGYGLQELEQVCECKELKSAGYNARQLKEAGYSAGRLRNCGFDACELRNAGFTAQEMKDGGFSDGELKGAGFSDAEIAKASGLPDGITADDVRKAGCGAAALAKLRQAGVSASAIRKISGCTAEQLKAAGYTAKELKDAGFSAADLRRAGFSAAELKDAGFTARDLLNAGFTPADLAKAGFSDAQIKAAQAELPPGITPQDVKNAGCDVEALKKEREAGVSAALIRQYAGCSAQALKAAGFTDADLANAGFTPAQISAATPLSDAEIKAAGCDPDKLKKLFSAGVSAKRIKELNGCSAEALKAAGYDAQSLLAAGFTPQELLAAGFTPKQLEDAGLNPVSIIADGRVADCSVESLKKARAAGVSALTIKQTLGCSAAALKAAGYTAKELKDAGFTAAELKAAGFSAKELKDAGFTAKELRDAGFSAQELKDVGFSAKDLKDAGFSAAELKAAGFTAAQLKAAGFSAKDLKDAGFSAAELKAAGFSAKELKDAGFSASDLKNAGFSAKELKDAGFSASDLKSAGFSASELKNAGYSADELKKAGYTSAELRNAGFSPQESAVAGLQGPDLQQLDSSITGIPSIPGATPRPTTSDAASSAEQLQAILQKQNEQLAEQKYQQEIQQRTSDMLTAATQLVQDWKQVETQVYTEGTEETKTSGGESAVPGTGTGTGSNNQPVDQGAVSAQNQAIIKTGDIMFAVLDTSVNSDEPGPILATIVTGKLKGSKLIGSFNLPSNADKMVITFNTMSIPGAEKTISISAYAIDPNTARTALASRTNHHYLMRYGSLFASSFLQGFGNAFQSANTTITIGGTGGGNNITVANGVGRSTLENAVIGLATVGKAWSQQAQQLFNTPTTVEVYSGTGLGILFTQDVTTI

Entity 8 Entity 8 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	Ew,Ex,Ey,Ez,Fa

MKVLPKLALANLVCFTTLSVFAQPADPSGQQTSTNTSNLVTYLTNLGKYLGYDITQSSKAPNPPYSQLFNSNVVQLVQNYAYNTFLGAIPVDAMSQSLMNFVTDKVQGNSLINNLANTTFKYQNFSAPSSGADGKITANGLIDQSTASAQTPTTPGIFSAPQITTSGTYLNDPVSQAVFNILGTPDYSFCMDNEQKNWLPNCNLMYQNLVMQNVIGTLPPAQTSGSTPAFYSYKYNQPLISQLNSNSLIAPLLMDTSASQSGQDSGLTAKSQAQQALNFIRYASAQVTPPSLPKLSAYSELWNQATAKPNSAGYNEVQQKQAAATLSSYFNNLRVYAAQTSVGVSNLYYILSKRLPQNMSADQSNANITSQALNEFNMATRRLFDPTASNTPGQPNQQWIKQINDASPATVQKEIAILLAEINYQMYLDRQIQERILLTNSIMLLQNLKAAQPTADFSSQGSPSEQ

Entity 9 Entity 9 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	Fb,Fc,Fd,Fe,Ff

MNKLAITVLLCFFPALALAENGALSFAPPASDLSVVFLGNLFGVVDGVLHGTGSQIMGNMFGVFNSAVLALGGIIIMYTLMVSTMNTAHEGQMLGQKWSSIWIPLRSTFGLALLIPKASGYCMMQVFFMWVIVQGVGAADKIWEAALSYLNRGGVIIQAQADPTKSLQAAGSSSSGVAKGALTILGGQICMLGLQKQLQAQRDLYLSQSKSPPCGGNPTPEMNTFCRTAIPDFISTVNFVKKQNDDTPKDLTANQPASFELDMPNFDKSSPFYFLNGICGTVKWNNISALNSTNQSDNKGLVTVGGAGSNSSMGANSLNITSSQLQTARLSRAIAIQQMYVTLSTVAQVMVNNDPAFSTTTSTGNSKNDFSAIAKQQFGVPYKSSGEVCTEYQQVCQTWGSVPSSTGSTTGVLFNGTEFLGAINDYNGIMMPTLNLIRQATSKEFDKKSRDFIAEANAKGWIMAGSYFFDLVKLNGSATEFADQFDTGTGLDKSSFDPTQLTKPFGKTCQDPYSLLCTWFQNKSDKLIQIQSLIDGVPALGQDGVKQPDLSDNPQRQSVSGPLSSTVYGFVNNSMMVQLPGQPGIKPLTFANLINFKVDTSLYYMKHQDFDCGRVKILFFSFCLGRMMGDLFYNYVFRYVYNFFLAIFGEMINSIVMAFLMIPLQGMKDIFIVGVQTLTQPGINPIVALANMGTMYINFSGTLWLTLLNMAVVSSLIPLFGIFIFALIMMAMPLLMAWIGTMVSIGFVTAYYIPVLPYMIFTFGSFAWLIAVIEAMVAAPIVALGVTHPEGNEAFGKGEFAIMILVNVFLRPSLMIIGYIAAIALSYVGVWILNAGFDHAISYIQSDQGIETWEKGTSSNDAKRFFQSAGNWTGAKMDTSQWDNFKDKLTGDYQSTALEGGYTGWAGVYAFFFSILIYTSMYLIIVQKAFTLIAHLPDKVLRWIGGSPESFGQETMQWGEEAKGRVEKAGEATYGAEKAIGDKLGAKGQEMLGKLGPQAKKISENAGDVSGKGKNSGGSQTGPSSKPDTGQQLGGSDSGTPTSTPPPE

▶

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	4.63 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	37503

In situ cryo-EM structure of PR and DotA-IcmX of the Legionella Dot/Icm T4SS machine at C1 symmetry

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

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9nh0__assembly_1__model_1

9nh0__assembly_1__model_1 | I(q)

9nh0__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 (9)

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

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

7. Citations (2)