6X6S image
Deposition Date 2020-05-29
Release Date 2020-10-07
Last Version Date 2024-03-06
Entry Detail
PDB ID:
6X6S
Keywords:
PROTEIN TRANSPORT
Title:
Cryo-EM Structure of the Helicobacter pylori OMC
Biological Source:
Source Organism:
Helicobacter pylori (Taxon ID: 210)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6X6S validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Type IV secretion system apparatus protein Cag3
Chain IDs:A (auth: AA), B (auth: AB), C (auth: AC), D (auth: AD), E (auth: AE), M (auth: BA), N (auth: BB), O (auth: BC), P (auth: BD), Q (auth: BE), Y (auth: CA), Z (auth: CB), AA (auth: CC), BA (auth: CD), CA (auth: CE), KA (auth: DA), LA (auth: DB), MA (auth: DC), NA (auth: DD), OA (auth: DE), WA (auth: EA), XA (auth: EB), YA (auth: EC), ZA (auth: ED), AB (auth: EE), IB (auth: FA), JB (auth: FB), KB (auth: FC), LB (auth: FD), MB (auth: FE), UB (auth: GA), VB (auth: GB), WB (auth: GC), XB (auth: GD), YB (auth: GE), GC (auth: HA), HC (auth: HB), IC (auth: HC), JC (auth: HD), KC (auth: HE), SC (auth: IA), TC (auth: IB), UC (auth: IC), VC (auth: ID), WC (auth: IE), ED (auth: JA), FD (auth: JB), GD (auth: JC), HD (auth: JD), ID (auth: JE), QD (auth: KA), RD (auth: KB), SD (auth: KC), TD (auth: KD), UD (auth: KE), CE (auth: LA), DE (auth: LB), EE (auth: LC), FE (auth: LD), GE (auth: LE), OE (auth: MA), PE (auth: MB), QE (auth: MC), RE (auth: MD), SE (auth: ME), AF (auth: NA), BF (auth: NB), CF (auth: NC), DF (auth: ND), EF (auth: NE)
Chain Length:481
Number of Molecules:70
Biological Source:Helicobacter pylori
Polymer Type:polypeptide(L)
Molecule:Type IV secretion system apparatus protein CagM
Chain IDs:F (auth: AM), K (auth: Am), R (auth: BM), W (auth: Bm), DA (auth: CM), IA (auth: Cm), PA (auth: DM), UA (auth: Dm), BB (auth: EM), GB (auth: Em), NB (auth: FM), SB (auth: Fm), ZB (auth: GM), EC (auth: Gm), LC (auth: HM), QC (auth: Hm), XC (auth: IM), CD (auth: Im), JD (auth: JM), OD (auth: Jm), VD (auth: KM), AE (auth: Km), HE (auth: LM), ME (auth: Lm), TE (auth: MM), YE (auth: Mm), FF (auth: NM), KF (auth: Nm)
Chain Length:376
Number of Molecules:28
Biological Source:Helicobacter pylori
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Type IV secretion system apparatus protein CagT
Gene (Uniprot):cag12
Chain IDs:G (auth: AT), L (auth: At), S (auth: BT), X (auth: Bt), EA (auth: CT), JA (auth: Ct), QA (auth: DT), VA (auth: Dt), CB (auth: ET), HB (auth: Et), OB (auth: FT), TB (auth: Ft), AC (auth: GT), FC (auth: Gt), MC (auth: HT), RC (auth: Ht), YC (auth: IT), DD (auth: It), KD (auth: JT), PD (auth: Jt), WD (auth: KT), BE (auth: Kt), IE (auth: LT), NE (auth: Lt), UE (auth: MT), ZE (auth: Mt), GF (auth: NT), LF (auth: Nt)
Chain Length:280
Number of Molecules:28
Biological Source:Helicobacter pylori
UniProt ID:Q6VRP0 Pfam ID:PF13117
Polymer Type:polypeptide(L)
Molecule:Unknown protein fragment
Chain IDs:H (auth: AU), T (auth: BU), FA (auth: CU), RA (auth: DU), DB (auth: EU), PB (auth: FU), BC (auth: GU), NC (auth: HU), ZC (auth: IU), LD (auth: JU), XD (auth: KU), JE (auth: LU), VE (auth: MU), HF (auth: NU)
Chain Length:160
Number of Molecules:14
Biological Source:Helicobacter pylori
Polymer Type:polypeptide(L)
Molecule:Type IV secretion system apparatus protein CagX
Chain IDs:I (auth: AX), U (auth: BX), GA (auth: CX), SA (auth: DX), EB (auth: EX), QB (auth: FX), CC (auth: GX), OC (auth: HX), AD (auth: IX), MD (auth: JX), YD (auth: KX), KE (auth: LX), WE (auth: MX), IF (auth: NX)
Chain Length:522
Number of Molecules:14
Biological Source:Helicobacter pylori
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cag pathogenicity island protein (Cag7)
Gene (Uniprot):HP_0527
Chain IDs:J (auth: AY), V (auth: BY), HA (auth: CY), TA (auth: DY), FB (auth: EY), RB (auth: FY), DC (auth: GY), PC (auth: HY), BD (auth: IY), ND (auth: JY), ZD (auth: KY), LE (auth: LY), XE (auth: MY), JF (auth: NY)
Chain Length:1927
Number of Molecules:14
Biological Source:Helicobacter pylori
UniProt ID:O25262 Pfam ID:PF14585, PF07337, PF03743
Ligand Molecules
NA
Primary Citation
Cryo-EM reveals species-specific components within the Helicobacter pylori Cag type IV secretion system core complex.
Elife 9 ? ? (2020)
PMID: 32876048 DOI: 10.7554/eLife.59495

Abstact

The pathogenesis of Helicobacter pylori-associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The H. pylori Cag T4SS includes a large membrane-spanning core complex containing five proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the H. pylori T4SS core complex is dependent on incorporation of interwoven species-specific components.

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Disease

Primary Citation of related structures
6X6S