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- PDB-5wq7: CryoEM structure of type II secretion system secretin GspD in E.c... -

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Basic information

Entry
Database: PDB / ID: 5wq7
TitleCryoEM structure of type II secretion system secretin GspD in E.coli K12
ComponentsPutative type II secretion system protein D
KeywordsPROTEIN TRANSPORT / Secretin family / C15 symmetry / T2SS
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily ...Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative secretin GspD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsYan, Z. / Yin, M. / Li, X.
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structural insights into the secretin translocation channel in the type II secretion system.
Authors: Zhaofeng Yan / Meng Yin / Dandan Xu / Yongqun Zhu / Xueming Li /
Abstract: The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. ...The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the GspD channel hinders the investigation of substrate translocation mechanism of T2SS. Here we report cryo-EM structures of two GspD channels (∼1 MDa), from Escherichia coli K12 and Vibrio cholerae, at ∼3 Å resolution. The structures reveal a pentadecameric channel architecture, wherein three rings of GspD N domains form the periplasmic channel. The secretin domain constitutes a novel double β-barrel channel, with at least 60 β-strands in each barrel, and is stabilized by S domains. The outer membrane channel is sealed by β-strand-enriched gates. On the basis of the partially open state captured, we proposed a detailed gate-opening mechanism. Our structures provide a structural basis for understanding the secretin superfamily and the mechanism of substrate translocation in T2SS.
History
DepositionNov 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
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Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Other
Category: atom_sites / cell ...atom_sites / cell / em_image_scans / em_software
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _em_software.name
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Putative type II secretion system protein D
B: Putative type II secretion system protein D
C: Putative type II secretion system protein D
D: Putative type II secretion system protein D
E: Putative type II secretion system protein D
F: Putative type II secretion system protein D
G: Putative type II secretion system protein D
H: Putative type II secretion system protein D
I: Putative type II secretion system protein D
J: Putative type II secretion system protein D
K: Putative type II secretion system protein D
L: Putative type II secretion system protein D
M: Putative type II secretion system protein D
N: Putative type II secretion system protein D
O: Putative type II secretion system protein D


Theoretical massNumber of molelcules
Total (without water)1,026,16215
Polymers1,026,16215
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area162450 Å2
ΔGint-736 kcal/mol
Surface area300980 Å2

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Components

#1: Protein
Putative type II secretion system protein D / T2SS Secretin GspD


Mass: 68410.789 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gspD, yheF, b3325, JW5707 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P45758
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Full length T2SS secretin GspD complexCOMPLEXall0RECOMBINANT
2Putative type II secretion system protein DCOMPLEXall1RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria) / Plasmid: pASK-IBA3c
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: OTHER
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10_2152: / Classification: refinement
EM software
IDNameCategory
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30659 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00955095
ELECTRON MICROSCOPYf_angle_d1.01174745
ELECTRON MICROSCOPYf_dihedral_angle_d10.01733780
ELECTRON MICROSCOPYf_chiral_restr0.2239090
ELECTRON MICROSCOPYf_plane_restr0.0059690

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