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- EMDB-49433: The cryo-EM structure of the periplasmic chaperone Skp from Neiss... -

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Basic information

Entry
Database: EMDB / ID: EMD-49433
TitleThe cryo-EM structure of the periplasmic chaperone Skp from Neisseria meningitidis
Map data
Sample
  • Complex: NmSkp
    • Protein or peptide: Outer membrane protein OmpH, putative
KeywordsPeriplasmic chaperone / Skp / Neisseria / OMP biogenesis / SLAM / CHAPERONE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsDubey S / Noinaj N
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49433.png

Downloads & links

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Map

FileDownload / File: emd_49433.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 270.08 Å		0.84 Å/pix.
x 320 pix.
= 270.08 Å		0.84 Å/pix.
x 320 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.212
Minimum - Maximum-0.32468128 - 0.79296327
Average (Standard dev.)0.00018143372 (±0.02372238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49433_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49433_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NmSkp

EntireName: NmSkp
Components
  • Complex: NmSkp
    • Protein or peptide: Outer membrane protein OmpH, putative

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Supramolecule #1: NmSkp

SupramoleculeName: NmSkp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 102 KDa

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Macromolecule #1: Outer membrane protein OmpH, putative

MacromoleculeName: Outer membrane protein OmpH, putative / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 17.171363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMGDTFQKI GFINTERIYL ESKQARKIQK TLDSEFSARQ DELQKLQREG LDLERQLAEG KLRNAKKAQA EEKWRGLVAA FRKKQAQFE EDYNLRRNEE FASLQQNANR VIVKIAKQEG YDVILQNVIY VNTQYDVTDS VIKEMNAR

UniProtKB: Outer membrane protein OmpH, putative

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8uam
PDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65553
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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