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- PDB-6x66: Legionella pneumophila dDot T4SS OMC -

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Basic information

Entry
Database: PDB / ID: 6x66
TitleLegionella pneumophila dDot T4SS OMC
Components
  • (Type IV secretion ...Secretion) x 2
  • DotC
  • DotD
  • Inner membrane lipoprotein YiaD
  • Outer membrane protein, OmpA family protein
KeywordsPROTEIN TRANSPORT / Secretion / T4SS / Dot
Function / homology
Function and homology information


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 superfamily / OmpA family / OmpA-like 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 superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type IV secretion protein IcmK / DotD / DotC / LphA (DotK) / Outer membrane protein, OmpA family protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDurie, C.L. / Sheedlo, M.J. / Chung, J.M. / Byrne, B.G. / Su, M. / Knight, T. / Swanson, M.S. / Lacy, D.B. / Ohi, M.D.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150027-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2T32DK007673 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Other privateSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI095755-10 United States
Other government1I01BX004447 United States
CitationJournal: Elife / Year: 2020
Title: Structural analysis of the Dot/Icm type IV secretion system core complex.
Authors: Clarissa L Durie / Michael J Sheedlo / Jeong Min Chung / Brenda G Byrne / Min Su / Thomas Knight / Michele Swanson / D Borden Lacy / Melanie D Ohi /
Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver ... is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conf / struct_sheet_range
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_torsion.auth_comp_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_id / _struct_conf.end_auth_comp_id / _struct_conf.end_label_comp_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_label_comp_id

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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
AX: Type IV secretion system unknown protein fragment
AY: Type IV secretion system unknown protein fragment
AZ: Type IV secretion system unknown protein fragment
Ad: DotD
BC: DotC
BD: DotD
BH: Type IV secretion protein IcmK
BK: Inner membrane lipoprotein YiaD
BX: Type IV secretion system unknown protein fragment
BY: Type IV secretion system unknown protein fragment
BZ: Type IV secretion system unknown protein fragment
Bd: DotD
CC: DotC
CD: DotD
CH: Type IV secretion protein IcmK
CK: Inner membrane lipoprotein YiaD
CX: Type IV secretion system unknown protein fragment
CY: Type IV secretion system unknown protein fragment
CZ: Type IV secretion system unknown protein fragment
Cd: DotD
DC: DotC
DD: DotD
DH: Type IV secretion protein IcmK
DK: Inner membrane lipoprotein YiaD
DX: Type IV secretion system unknown protein fragment
DY: Type IV secretion system unknown protein fragment
DZ: Type IV secretion system unknown protein fragment
Dd: DotD
EC: DotC
ED: DotD
EH: Type IV secretion protein IcmK
EK: Inner membrane lipoprotein YiaD
EX: Type IV secretion system unknown protein fragment
EY: Type IV secretion system unknown protein fragment
EZ: Type IV secretion system unknown protein fragment
Ed: DotD
FC: DotC
FD: DotD
FH: Type IV secretion protein IcmK
FK: Inner membrane lipoprotein YiaD
FX: Type IV secretion system unknown protein fragment
FY: Type IV secretion system unknown protein fragment
FZ: Type IV secretion system unknown protein fragment
Fd: DotD
GC: DotC
GD: DotD
GH: Type IV secretion protein IcmK
GK: Inner membrane lipoprotein YiaD
GX: Type IV secretion system unknown protein fragment
GY: Type IV secretion system unknown protein fragment
GZ: Type IV secretion system unknown protein fragment
Gd: DotD
HC: DotC
HD: DotD
HH: Type IV secretion protein IcmK
HK: Inner membrane lipoprotein YiaD
HX: Type IV secretion system unknown protein fragment
HY: Type IV secretion system unknown protein fragment
HZ: Type IV secretion system unknown protein fragment
Hd: DotD
IC: DotC
ID: DotD
IH: Type IV secretion protein IcmK
IK: Inner membrane lipoprotein YiaD
IX: Type IV secretion system unknown protein fragment
IY: Type IV secretion system unknown protein fragment
IZ: Type IV secretion system unknown protein fragment
Id: DotD
JC: DotC
JD: DotD
JH: Type IV secretion protein IcmK
JK: Inner membrane lipoprotein YiaD
JX: Type IV secretion system unknown protein fragment
JY: Type IV secretion system unknown protein fragment
JZ: Type IV secretion system unknown protein fragment
Jd: DotD
KC: DotC
KD: DotD
KH: Type IV secretion protein IcmK
KK: Inner membrane lipoprotein YiaD
KX: Type IV secretion system unknown protein fragment
KY: Type IV secretion system unknown protein fragment
KZ: Type IV secretion system unknown protein fragment
Kd: DotD
LC: DotC
LD: DotD
LH: Type IV secretion protein IcmK
LK: Inner membrane lipoprotein YiaD
LX: Type IV secretion system unknown protein fragment
LY: Type IV secretion system unknown protein fragment
LZ: Type IV secretion system unknown protein fragment
Ld: DotD
MC: DotC
MD: DotD
MH: Type IV secretion protein IcmK
MK: Inner membrane lipoprotein YiaD
MX: Type IV secretion system unknown protein fragment
MY: Type IV secretion system unknown protein fragment
MZ: Type IV secretion system unknown protein fragment
Md: DotD
AA: Outer membrane protein, OmpA family protein
BA: Outer membrane protein, OmpA family protein
CA: Outer membrane protein, OmpA family protein
DA: Outer membrane protein, OmpA family protein
EA: Outer membrane protein, OmpA family protein
FA: Outer membrane protein, OmpA family protein
GA: Outer membrane protein, OmpA family protein
HA: Outer membrane protein, OmpA family protein
IA: Outer membrane protein, OmpA family protein
JA: Outer membrane protein, OmpA family protein
KA: Outer membrane protein, OmpA family protein
LA: Outer membrane protein, OmpA family protein
QA: Outer membrane protein, OmpA family protein


Theoretical massNumber of molelcules
Total (without water)3,143,774117
Polymers3,143,774117
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area318090 Å2
ΔGint-1659 kcal/mol
Surface area647330 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "HA"
d_2ens_1chain "BA"
d_3ens_1chain "CA"
d_4ens_1chain "DA"
d_5ens_1chain "EA"
d_6ens_1chain "FA"
d_7ens_1chain "GA"
d_8ens_1chain "IA"
d_9ens_1chain "AA"
d_10ens_1chain "JA"
d_11ens_1chain "KA"
d_12ens_1chain "LA"
d_13ens_1chain "QA"
d_1ens_2chain "JC"
d_2ens_2chain "BC"
d_3ens_2chain "CC"
d_4ens_2chain "DC"
d_5ens_2chain "EC"
d_6ens_2chain "FC"
d_7ens_2chain "GC"
d_8ens_2chain "HC"
d_9ens_2chain "IC"
d_10ens_2chain "AC"
d_11ens_2chain "KC"
d_12ens_2chain "LC"
d_13ens_2chain "MC"
d_1ens_3chain "GH"
d_2ens_3chain "BH"
d_3ens_3chain "CH"
d_4ens_3chain "DH"
d_5ens_3chain "EH"
d_6ens_3chain "FH"
d_7ens_3chain "AH"
d_8ens_3chain "HH"
d_9ens_3chain "IH"
d_10ens_3chain "JH"
d_11ens_3chain "KH"
d_12ens_3chain "LH"
d_13ens_3chain "MH"
d_1ens_4chain "JK"
d_2ens_4chain "BK"
d_3ens_4chain "CK"
d_4ens_4chain "DK"
d_5ens_4chain "EK"
d_6ens_4chain "FK"
d_7ens_4chain "GK"
d_8ens_4chain "HK"
d_9ens_4chain "IK"
d_10ens_4chain "MK"
d_11ens_4chain "KK"
d_12ens_4chain "LK"
d_13ens_4chain "AK"
d_1ens_5chain "HX"
d_2ens_5chain "BX"
d_3ens_5chain "CX"
d_4ens_5chain "DX"
d_5ens_5chain "EX"
d_6ens_5chain "FX"
d_7ens_5chain "AX"
d_8ens_5chain "GX"
d_9ens_5chain "IX"
d_10ens_5chain "JX"
d_11ens_5chain "KX"
d_12ens_5chain "LX"
d_13ens_5chain "MX"
d_1ens_6chain "HY"
d_2ens_6chain "BY"
d_3ens_6chain "CY"
d_4ens_6chain "DY"
d_5ens_6chain "EY"
d_6ens_6chain "FY"
d_7ens_6chain "AY"
d_8ens_6chain "JY"
d_9ens_6chain "IY"
d_10ens_6chain "GY"
d_11ens_6chain "KY"
d_12ens_6chain "LY"
d_13ens_6chain "MY"
d_1ens_7chain "KZ"
d_2ens_7chain "BZ"
d_3ens_7chain "CZ"
d_4ens_7chain "DZ"
d_5ens_7chain "EZ"
d_6ens_7chain "FZ"
d_7ens_7chain "GZ"
d_8ens_7chain "HZ"
d_9ens_7chain "IZ"
d_10ens_7chain "JZ"
d_11ens_7chain "AZ"
d_12ens_7chain "LZ"
d_13ens_7chain "MZ"

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7

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Components

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Protein , 4 types, 65 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
#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
#6: 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

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Type IV secretion ... , 2 types, 52 molecules AHBHCHDHEHFHGHHHIHJHKHLHMHAXAYAZBXBYBZCXCYCZDXDYDZEXEYEZFXFY...

#3: Protein
Type IV secretion protein IcmK / Secretion


Mass: 38958.926 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A2S6FBG9
#5: Protein ...
Type IV secretion system unknown protein fragment / Secretion


Mass: 28102.492 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria)

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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: dDotG Dot/Icm T4SS / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Legionella pneumophila (bacteria)
Buffer solutionpH: 7
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 FIELDBright-field microscopy
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6342 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 341.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0164110734
ELECTRON MICROSCOPYf_angle_d1.6995151086
ELECTRON MICROSCOPYf_chiral_restr0.080218187
ELECTRON MICROSCOPYf_plane_restr0.010119721
ELECTRON MICROSCOPYf_dihedral_angle_d22.340216471

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