SAXSdb — 6x66

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

DotC

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 117	DotD × 26 （O52183） Type IV secretion protein IcmK × 13 （A0A2S6FBG9） Inner membrane lipoprotein YiaD × 13 （O53086） Type IV secretion system unknown protein fragment × 39 Outer membrane protein, OmpA family protein × 13 （Q5ZXS4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52184_LEGPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AC； PDBConstruct 1–303； UniProt 1–303 Author chain BC； PDBConstruct 1–303； UniProt 1–303 Author chain CC； PDBConstruct 1–303； UniProt 1–303 Author chain DC； PDBConstruct 1–303； UniProt 1–303 Author chain EC； PDBConstruct 1–303； UniProt 1–303 Author chain FC； PDBConstruct 1–303； UniProt 1–303 Author chain GC； PDBConstruct 1–303； UniProt 1–303 Author chain HC； PDBConstruct 1–303； UniProt 1–303 Author chain IC； PDBConstruct 1–303； UniProt 1–303 Author chain JC； PDBConstruct 1–303； UniProt 1–303 Author chain KC； PDBConstruct 1–303； UniProt 1–303 Author chain LC； PDBConstruct 1–303； UniProt 1–303 Author chain MC； PDBConstruct 1–303； UniProt 1–303

DotD

OrganismNot specified

UniProt O52183

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 117	DotC × 13 （O52184） Type IV secretion protein IcmK × 13 （A0A2S6FBG9） Inner membrane lipoprotein YiaD × 13 （O53086） Type IV secretion system unknown protein fragment × 39 Outer membrane protein, OmpA family protein × 13 （Q5ZXS4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52183_LEGPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain AD； PDBConstruct 1–163； UniProt 1–163 Author chain Ad； PDBConstruct 1–163； UniProt 1–163 Author chain BD； PDBConstruct 1–163； UniProt 1–163 Author chain Bd； PDBConstruct 1–163； UniProt 1–163 Author chain CD； PDBConstruct 1–163； UniProt 1–163 Author chain Cd； PDBConstruct 1–163； UniProt 1–163 Author chain DD； PDBConstruct 1–163； UniProt 1–163 Author chain Dd； PDBConstruct 1–163； UniProt 1–163 Author chain ED； PDBConstruct 1–163； UniProt 1–163 Author chain Ed； PDBConstruct 1–163； UniProt 1–163 Author chain FD； PDBConstruct 1–163； UniProt 1–163 Author chain Fd； PDBConstruct 1–163； UniProt 1–163 Author chain GD； PDBConstruct 1–163； UniProt 1–163 Author chain Gd； PDBConstruct 1–163； UniProt 1–163 Author chain HD； PDBConstruct 1–163； UniProt 1–163 Author chain Hd； PDBConstruct 1–163； UniProt 1–163 Author chain ID； PDBConstruct 1–163； UniProt 1–163 Author chain Id； PDBConstruct 1–163； UniProt 1–163 Author chain JD； PDBConstruct 1–163； UniProt 1–163 Author chain Jd； PDBConstruct 1–163； UniProt 1–163 Author chain KD； PDBConstruct 1–163； UniProt 1–163 Author chain Kd； PDBConstruct 1–163； UniProt 1–163 Author chain LD； PDBConstruct 1–163； UniProt 1–163 Author chain Ld； PDBConstruct 1–163； UniProt 1–163 Author chain MD； PDBConstruct 1–163； UniProt 1–163 Author chain Md； PDBConstruct 1–163； UniProt 1–163

Type IV secretion protein IcmK

OrganismNot specified

UniProt A0A2S6FBG9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 117	DotC × 13 （O52184） DotD × 26 （O52183） Inner membrane lipoprotein YiaD × 13 （O53086） Type IV secretion system unknown protein fragment × 39 Outer membrane protein, OmpA family protein × 13 （Q5ZXS4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2S6FBG9_LEGPN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain AH； PDBConstruct 1–361； UniProt 1–361 Author chain BH； PDBConstruct 1–361； UniProt 1–361 Author chain CH； PDBConstruct 1–361； UniProt 1–361 Author chain DH； PDBConstruct 1–361； UniProt 1–361 Author chain EH； PDBConstruct 1–361； UniProt 1–361 Author chain FH； PDBConstruct 1–361； UniProt 1–361 Author chain GH； PDBConstruct 1–361； UniProt 1–361 Author chain HH； PDBConstruct 1–361； UniProt 1–361 Author chain IH； PDBConstruct 1–361； UniProt 1–361 Author chain JH； PDBConstruct 1–361； UniProt 1–361 Author chain KH； PDBConstruct 1–361； UniProt 1–361 Author chain LH； PDBConstruct 1–361； UniProt 1–361 Author chain MH； PDBConstruct 1–361； UniProt 1–361

Inner membrane lipoprotein YiaD

OrganismNot specified

UniProt O53086

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 117	DotC × 13 （O52184） DotD × 26 （O52183） Type IV secretion protein IcmK × 13 （A0A2S6FBG9） Type IV secretion system unknown protein fragment × 39 Outer membrane protein, OmpA family protein × 13 （Q5ZXS4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O53086_LEGPN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain AK； PDBConstruct 1–189； UniProt 1–189 Author chain BK； PDBConstruct 1–189； UniProt 1–189 Author chain CK； PDBConstruct 1–189； UniProt 1–189 Author chain DK； PDBConstruct 1–189； UniProt 1–189 Author chain EK； PDBConstruct 1–189； UniProt 1–189 Author chain FK； PDBConstruct 1–189； UniProt 1–189 Author chain GK； PDBConstruct 1–189； UniProt 1–189 Author chain HK； PDBConstruct 1–189； UniProt 1–189 Author chain IK； PDBConstruct 1–189； UniProt 1–189 Author chain JK； PDBConstruct 1–189； UniProt 1–189 Author chain KK； PDBConstruct 1–189； UniProt 1–189 Author chain LK； PDBConstruct 1–189； UniProt 1–189 Author chain MK； PDBConstruct 1–189； UniProt 1–189

Outer membrane protein, OmpA family protein

OrganismNot specified

UniProt Q5ZXS4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 117	DotC × 13 （O52184） DotD × 26 （O52183） Type IV secretion protein IcmK × 13 （A0A2S6FBG9） Inner membrane lipoprotein YiaD × 13 （O53086） Type IV secretion system unknown protein fragment × 39	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZXS4_LEGPH
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain AA； PDBConstruct 1–249； UniProt 1–249 Author chain BA； PDBConstruct 1–249； UniProt 1–249 Author chain CA； PDBConstruct 1–249； UniProt 1–249 Author chain DA； PDBConstruct 1–249； UniProt 1–249 Author chain EA； PDBConstruct 1–249； UniProt 1–249 Author chain FA； PDBConstruct 1–249； UniProt 1–249 Author chain GA； PDBConstruct 1–249； UniProt 1–249 Author chain HA； PDBConstruct 1–249； UniProt 1–249 Author chain IA； PDBConstruct 1–249； UniProt 1–249 Author chain JA； PDBConstruct 1–249； UniProt 1–249 Author chain KA； PDBConstruct 1–249； UniProt 1–249 Author chain LA； PDBConstruct 1–249； UniProt 1–249 Author chain QA； PDBConstruct 1–249； UniProt 1–249

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	6x66
Deposition date deposition_date	2020-05-27
Structure title title	Legionella pneumophila dDot T4SS OMC
Keywords keywords	Secretion, T4SS, Dot, 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.

6x66__assembly_1__model_1

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

Download this curve (.dat)

6x66__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6x66__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	126.80 Å
Total Rg	126.30 Å
Atom count	109070
Residues	15548
Excluded volume	1916900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6x66__assembly_1__model_1`	117-meric （117）	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	DotC
Molecular weight formula_weight	34162.4 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC
Atom count atom_count	109070

MRKFILSLSILLSALLVACSSRNHYGDTGSLAGLQAMADSKYTRAQKKQKMGKIREMALKETALSVGAQAGLAWRAKIIDEQLNKQARNLDAIYDFNSLVLEHNILPPVLLEGRNTLNLADAQSIRISDRTYKVAKQAHFITTPPTWRQYLWMDYVKPEAPNVTLLPKTKAEKEIWCIYTERGWKNGIDQANTILEENIARIKEDFGGMILYRKLLAMNMVSPPYVSHTDLGVTGDGSEIHIDDRVLRITALPELNVNSAEWRAAVAKDENALERFKNMEKLANQAKIVITNKSWQPIIAPVS

Entity 2 Entity 2 polymer

Description description	DotD
Molecular weight formula_weight	17860.7 kDa
Source method src_method	nat
Copy count entity_count	26

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AD,Ad,BD,Bd,CD,Cd,DD,Dd,ED,Ed,FD,Fd,GD,Gd,HD,Hd,ID,Id,JD,Jd,KD,Kd,LD,Ld,MD,Md

MNNNKIVIMFIFSALLAGCAGTMKFKKPPINNPSDDATIKLAEAAVSVSDSMLEMAKVEKVITPPSKDNTLTIPNAYNLQARASVDWSGPIEELTARIAKAAHFRFRVLGKSPSVPVLISISTKDESLAEILRDIDYQAGKKASIHVYPNSQVVELRYAKIYS

Entity 3 Entity 3 polymer

Description description	Type IV secretion protein IcmK
Molecular weight formula_weight	38958.9 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AH,BH,CH,DH,EH,FH,GH,HH,IH,JH,KH,LH,MH

MMKKYDQLCKYCLVIGLTFSMSCSIYAADQSDDAQQALQQLRMLQQKLSQNPSPDAQSGAGDGGDNAASDSTQQPNQSGQANAPAANQTATAGGDGQIISQDDAEVIDKKAFKDMTRNLYPLNPEQVVKLKQIYETSEYAKAATPGTPPKPTATSQFVNLSPGSTPPVIRLSQGFVSSLVFLDSTGAPWPIAAYDLGDPSSFNIQWDKTSNTLMIQATKLYNYGNLAVRLRGLNTPVMLTLIPGQKAVDYRVDLRVQGYGPNAKSMPTEEGIPPSANDLLLHVLEGVPPPGSRRLVVSGGDARAWLSNEKMYVRTNLTILSPGWLASMTSADGTHAYEMQKSPVLLVSWHGKVMQLKVEGL

Entity 4 Entity 4 polymer

Description description	Inner membrane lipoprotein YiaD
Molecular weight formula_weight	21096.5 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AK,BK,CK,DK,EK,FK,GK,HK,IK,JK,KK,LK,MK

MRSLRTNYIYVLFKTTGLLFLLLLSACNRSGYIPENEVPKLPCRVDGACDATIIKMMTDLNKKGIKVASVGQNYLISIPASALFADQSPRLNWASYSLLNEIAAFLKQFRKIAITVTSYSSKYVSVKRERALTLARSRVVSEYLWSQGVDSRIIFTQGLGSDKPITSYTLGGDRSPNARVEITFRRAVA

Entity 5 Entity 5 polymer

Description description	Type IV secretion system unknown protein fragment
Molecular weight formula_weight	28102.5 kDa
Source method src_method	nat
Copy count entity_count	39

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AX,AY,AZ,BX,BY,BZ,CX,CY,CZ,DX,DY,DZ,EX,EY,EZ,FX,FY,FZ,GX,GY,GZ,HX,HY,HZ,IX,IY,IZ,JX,JY,JZ,KX,KY,KZ,LX,LY,LZ,MX,MY,MZ

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 6 Entity 6 polymer

Description description	Outer membrane protein, OmpA family protein
Molecular weight formula_weight	27582.0 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,QA

MRNLMRCLIMIKSLIKGVDMSRKLAKTRILGYGLMICFLAGCFHPPYNNFQPDRRAVKRVGVDTGIGAVAGAIASGTASGTLIGAAAGGTVGLVASIYRDSKRKIIRDLQKQDIQYVEYGDTRTLIIPTDKYFMFSSPRLNEICYPGLNNVIRLLNFYPQSTIYVAGFTDNVGSRSHKRKLSQAQAETMMTFLWANGIAAKRLKAEGYGDKNAISDNAIIHGSAQNRRIEIQWFTSPAQPPQPQMAYVK

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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	4.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	6342

Legionella pneumophila dDot T4SS OMC

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

DotC

State in the Current Structure

Other States of the Same Protein in the Database

DotD

State in the Current Structure

Other States of the Same Protein in the Database

Type IV secretion protein IcmK

State in the Current Structure

Other States of the Same Protein in the Database

Inner membrane lipoprotein YiaD

State in the Current Structure

Other States of the Same Protein in the Database

Outer membrane protein, OmpA family protein

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

6x66__assembly_1__model_1

6x66__assembly_1__model_1 | I(q)

6x66__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

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

7. Citations (1)

Legionella pneumophila dDot T4SS OMC

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

DotC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DotD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Type IV secretion protein IcmK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inner membrane lipoprotein YiaD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Outer membrane protein, OmpA family 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

6x66__assembly_1__model_1

6x66__assembly_1__model_1 | I(q)

6x66__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

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

7. Citations (1)