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- PDB-7muc: Legionella pneumophila Dot/Icm T4SS C1 Reconstruction -

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Basic information

Entry
Database: PDB / ID: 7muc
TitleLegionella pneumophila Dot/Icm T4SS C1 Reconstruction
Components
  • (Unknown protein ...) x 2
  • DUF2807 domain-containing protein
  • DotC
  • DotD
  • DotF
  • IcmE protein
  • Inner membrane lipoprotein YiaD
  • Neurogenic locus notch
  • Outer membrane protein, OmpA family protein
  • Type IV secretion protein IcmK
KeywordsTRANSLOCASE / Legionella / Dot/Icm / Secretion / T4SS
Function / homology
Function and homology information


: / : / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Putative type IV secretory system protein / Type IV secretory system, conjugal DNA-protein transfer / DotD protein / DotD superfamily / DotD protein / Putative outer membrane core complex of type IVb secretion ...: / : / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Putative type IV secretory system protein / Type IV secretory system, conjugal DNA-protein transfer / DotD protein / DotD superfamily / DotD protein / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative auto-transporter adhesin head GIN domain-containing protein / Neurogenic locus notch / Type IV secretion protein IcmK / DotD / DotC / Inner membrane lipoprotein YiaD / IcmE protein / DotF / Outer membrane protein, OmpA family protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSheedlo, M.J. / Durie, C.L. / Swanson, M. / Lacy, D.B. / Ohi, M.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI118932 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI150027-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2T32DK007673 United States
Other governmentS10OD020011 United States
CitationJournal: Elife / Year: 2021
Title: Cryo-EM reveals new species-specific proteins and symmetry elements in the Dot/Icm T4SS.
Authors: Michael J Sheedlo / Clarissa L Durie / Jeong Min Chung / Louise Chang / Jacquelyn Roberts / Michele Swanson / Dana Borden Lacy / Melanie D Ohi /
Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins ... is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure.
History
DepositionMay 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
AC: DotC
AD: DotD
AF: DotF
AG: IcmE protein
AH: Type IV secretion protein IcmK
AK: Inner membrane lipoprotein YiaD
AL: Outer membrane protein, OmpA family protein
AM: DUF2807 domain-containing protein
AN: Neurogenic locus notch
AU: Unknown protein fragment
AX: Unknown protein fragment
Ad: DotD
Af: DotF
BC: DotC
BD: DotD
BF: DotF
BG: IcmE protein
BH: Type IV secretion protein IcmK
BK: Inner membrane lipoprotein YiaD
BL: Outer membrane protein, OmpA family protein
BM: DUF2807 domain-containing protein
BN: Neurogenic locus notch
BU: Unknown protein fragment
BX: Unknown protein fragment
Bd: DotD
Bf: DotF
CC: DotC
CD: DotD
CF: DotF
CG: IcmE protein
CH: Type IV secretion protein IcmK
CK: Inner membrane lipoprotein YiaD
CL: Outer membrane protein, OmpA family protein
CM: DUF2807 domain-containing protein
CN: Neurogenic locus notch
CU: Unknown protein fragment
CX: Unknown protein fragment
Cd: DotD
Cf: DotF
DC: DotC
DD: DotD
DF: DotF
DG: IcmE protein
DH: Type IV secretion protein IcmK
DK: Inner membrane lipoprotein YiaD
DL: Outer membrane protein, OmpA family protein
DM: DUF2807 domain-containing protein
DN: Neurogenic locus notch
DU: Unknown protein fragment
DX: Unknown protein fragment
Dd: DotD
Df: DotF
EC: DotC
ED: DotD
EF: DotF
EG: IcmE protein
EH: Type IV secretion protein IcmK
EK: Inner membrane lipoprotein YiaD
EL: Outer membrane protein, OmpA family protein
EM: DUF2807 domain-containing protein
EN: Neurogenic locus notch
EU: Unknown protein fragment
EX: Unknown protein fragment
Ed: DotD
Ef: DotF
FC: DotC
FD: DotD
FF: DotF
FG: IcmE protein
FH: Type IV secretion protein IcmK
FK: Inner membrane lipoprotein YiaD
FL: Outer membrane protein, OmpA family protein
FM: DUF2807 domain-containing protein
FN: Neurogenic locus notch
FU: Unknown protein fragment
FX: Unknown protein fragment
Fd: DotD
Ff: DotF
GC: DotC
GD: DotD
GF: DotF
GG: IcmE protein
GH: Type IV secretion protein IcmK
GK: Inner membrane lipoprotein YiaD
GL: Outer membrane protein, OmpA family protein
GM: DUF2807 domain-containing protein
GN: Neurogenic locus notch
GU: Unknown protein fragment
GX: Unknown protein fragment
Gd: DotD
Gf: DotF
HC: DotC
HD: DotD
HF: DotF
HG: IcmE protein
HH: Type IV secretion protein IcmK
HK: Inner membrane lipoprotein YiaD
HL: Outer membrane protein, OmpA family protein
HM: DUF2807 domain-containing protein
HN: Neurogenic locus notch
HU: Unknown protein fragment
HX: Unknown protein fragment
Hd: DotD
Hf: DotF
IC: DotC
ID: DotD
IF: DotF
IG: IcmE protein
IH: Type IV secretion protein IcmK
IK: Inner membrane lipoprotein YiaD
IL: Outer membrane protein, OmpA family protein
IM: DUF2807 domain-containing protein
IN: Neurogenic locus notch
IU: Unknown protein fragment
IX: Unknown protein fragment
Id: DotD
If: DotF
JC: DotC
JD: DotD
JF: DotF
JG: IcmE protein
JH: Type IV secretion protein IcmK
JK: Inner membrane lipoprotein YiaD
JL: Outer membrane protein, OmpA family protein
JM: DUF2807 domain-containing protein
JN: Neurogenic locus notch
JU: Unknown protein fragment
JX: Unknown protein fragment
Jd: DotD
Jf: DotF
KC: DotC
KD: DotD
KF: DotF
KG: IcmE protein
KH: Type IV secretion protein IcmK
KK: Inner membrane lipoprotein YiaD
KL: Outer membrane protein, OmpA family protein
KM: DUF2807 domain-containing protein
KN: Neurogenic locus notch
KU: Unknown protein fragment
KX: Unknown protein fragment
Kd: DotD
Kf: DotF
LC: DotC
LD: DotD
LF: DotF
LG: IcmE protein
LH: Type IV secretion protein IcmK
LK: Inner membrane lipoprotein YiaD
LL: Outer membrane protein, OmpA family protein
LM: DUF2807 domain-containing protein
LN: Neurogenic locus notch
LU: Unknown protein fragment
LX: Unknown protein fragment
Ld: DotD
Lf: DotF
MC: DotC
MD: DotD
MF: DotF
MG: IcmE protein
MH: Type IV secretion protein IcmK
MK: Inner membrane lipoprotein YiaD
ML: Outer membrane protein, OmpA family protein
MM: DUF2807 domain-containing protein
MN: Neurogenic locus notch
MU: Unknown protein fragment
MX: Unknown protein fragment
Md: DotD
Mf: DotF
VF: DotF
VG: IcmE protein
VH: Type IV secretion protein IcmK
VX: Unknown protein fragment
WF: DotF
WG: IcmE protein
WH: Type IV secretion protein IcmK
WX: Unknown protein fragment
XF: DotF
XG: IcmE protein
XH: Type IV secretion protein IcmK
XX: Unknown protein fragment
YF: DotF
YG: IcmE protein
YH: Type IV secretion protein IcmK
YX: Unknown protein fragment
ZF: DotF
ZG: IcmE protein
ZH: Type IV secretion protein IcmK
ZX: Unknown protein fragment


Theoretical massNumber of molelcules
Total (without water)5,836,685189
Polymers5,836,685189
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area637760 Å2
ΔGint-3562 kcal/mol
Surface area992290 Å2

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Components

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Protein , 9 types, 158 molecules ACBCCCDCECFCGCHCICJCKCLCMCADAdBDBdCDCdDDDdEDEdFDFdGDGdHDHdID...

#1: Protein
DotC / Type IV secretion system protein DotC


Mass: 34162.441 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O52184
#2: Protein ...
DotD


Mass: 17860.678 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O52183
#3: Protein ...
DotF / IcmG protein / Type IV secretion protein IcmG


Mass: 29729.969 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O54615
#4: Protein
IcmE protein / Type IV secretion protein IcmE


Mass: 107911.891 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O53087
#5: Protein
Type IV secretion protein IcmK


Mass: 38958.926 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A2S6FBG9
#6: Protein
Inner membrane lipoprotein YiaD / LphA (DotK) / LphA protein / OmpA family protein


Mass: 21096.492 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O53086
#7: Protein
Outer membrane protein, OmpA family protein


Mass: 27582.047 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: Q5ZXS4
#8: Protein
DUF2807 domain-containing protein


Mass: 36095.367 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A2S6F0F8
#9: Protein
Neurogenic locus notch


Mass: 13598.854 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A2S6FAR3

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Unknown protein ... , 2 types, 31 molecules AUBUCUDUEUFUGUHUIUJUKULUMUAXBXCXDXEXFXGXHXIXJXKXLXMXVXWXXXYXZX

#10: Protein/peptide
Unknown protein fragment


Mass: 783.958 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria)
#11: Protein/peptide
Unknown protein fragment


Mass: 4103.049 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Legionella pneumophila Dot/Icm T4SS C1 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Legionella pneumophila (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122+SVNrefinement
PHENIX1.19.1_4122+SVNrefinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136818 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 163.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0119183700
ELECTRON MICROSCOPYf_angle_d1.8155249034
ELECTRON MICROSCOPYf_chiral_restr0.086528470
ELECTRON MICROSCOPYf_plane_restr0.009631909
ELECTRON MICROSCOPYf_dihedral_angle_d15.741567563

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