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- PDB-7mud: Legionella pneumophila Dot/Icm T4SS OMC -

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Basic information

Entry
Database: PDB / ID: 7mud
TitleLegionella pneumophila Dot/Icm T4SS OMC
Components
  • DUF2807 domain-containing protein
  • DotC
  • DotD
  • DotF
  • Inner membrane lipoprotein YiaD
  • Neurogenic locus notch
  • Outer membrane protein, OmpA family protein
  • Type IV secretion protein IcmK
  • Unknown protein fragment
KeywordsTRANSLOCASE / 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 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 / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 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 / LphA (DotK) / DotF / Outer membrane protein, OmpA family protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020011 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 2.0Apr 20, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_validate_torsion
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _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 / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_validate_torsion.auth_comp_id
Revision 2.1Nov 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
AC: DotC
AD: DotD
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
Ad: DotD
Af: DotF
BC: DotC
BD: DotD
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
Bd: DotD
Bf: DotF
CC: DotC
CD: DotD
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
Cd: DotD
Cf: DotF
DC: DotC
DD: DotD
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
Dd: DotD
Df: DotF
EC: DotC
ED: DotD
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
Ed: DotD
Ef: DotF
FC: DotC
FD: DotD
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
Fd: DotD
Ff: DotF
GC: DotC
GD: DotD
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
Gd: DotD
Gf: DotF
HC: DotC
HD: DotD
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
Hd: DotD
Hf: DotF
IC: DotC
ID: DotD
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
Id: DotD
If: DotF
JC: DotC
JD: DotD
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
Jd: DotD
Jf: DotF
KC: DotC
KD: DotD
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
Kd: DotD
Kf: DotF
LC: DotC
LD: DotD
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
Ld: DotD
Lf: DotF
MC: DotC
MD: DotD
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
Md: DotD
Mf: DotF


Theoretical massNumber of molelcules
Total (without water)3,090,482130
Polymers3,090,482130
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area448630 Å2
ΔGint-2413 kcal/mol
Surface area717930 Å2

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Components

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Protein , 8 types, 117 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
Type IV secretion protein IcmK


Mass: 38958.926 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A2S6FBG9
#4: 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
#5: 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
#6: 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
#7: 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
#9: Protein
DotF / IcmG protein / Type IV secretion protein IcmG


Mass: 29729.969 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O54615

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Protein/peptide , 1 types, 13 molecules AUBUCUDUEUFUGUHUIUJUKULUMU

#8: 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)

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Details

Has protein modificationY
Sequence detailsThe protein fragment sequence could not be directly identified as the sample was purified from a ...The protein fragment sequence could not be directly identified as the sample was purified from a native source.

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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 OMC / 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
NameVersionClassificationNB
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84886 / 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: 55.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034137280
ELECTRON MICROSCOPYf_angle_d0.7395185796
ELECTRON MICROSCOPYf_chiral_restr0.051521021
ELECTRON MICROSCOPYf_plane_restr0.005523738
ELECTRON MICROSCOPYf_dihedral_angle_d5.086418824

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