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- PDB-9nhx: The cryo-EM structure of the periplasmic chaperone Skp from Neiss... -

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Basic information

Entry
Database: PDB / ID: 9nhx
TitleThe cryo-EM structure of the periplasmic chaperone Skp from Neisseria meningitidis
ComponentsOuter membrane protein OmpH, putative
KeywordsCHAPERONE / Periplasmic chaperone / Skp / Neisseria / OMP biogenesis / SLAM
Function / homologyChaperone protein Skp / Skp domain superfamily / Outer membrane protein (OmpH-like) / Outer membrane protein (OmpH-like) / : / protein stabilization / cytosol / Outer membrane protein OmpH, putative
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsDubey, S. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
CitationJournal: To Be Published
Title: The cryo-EM structure of the periplasmic chaperone Skp from Neisseria meningitidis
Authors: Dubey, S. / Noinaj, N.
History
DepositionFeb 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein OmpH, putative
B: Outer membrane protein OmpH, putative
C: Outer membrane protein OmpH, putative
D: Outer membrane protein OmpH, putative
E: Outer membrane protein OmpH, putative
F: Outer membrane protein OmpH, putative


Theoretical massNumber of molelcules
Total (without water)103,0286
Polymers103,0286
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Outer membrane protein OmpH, putative


Mass: 17171.363 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: skp, CNQ34_05000, COI09_03455, ERS514591_00664, ERS514851_00425, NCTC8554_02345
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Y6QFF4
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

ComponentName: NmSkp / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.102 MDa / Experimental value: NO
Source (natural)Organism: Neisseria meningitidis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18rc1_3777: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65553 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046798
ELECTRON MICROSCOPYf_angle_d0.9199132
ELECTRON MICROSCOPYf_dihedral_angle_d7.982918
ELECTRON MICROSCOPYf_chiral_restr0.0471008
ELECTRON MICROSCOPYf_plane_restr0.0061218

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