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- PDB-10am: C. Jejuni Simpl-Like Protein -

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Basic information

Entry
Database: PDB / ID: 10am
TitleC. Jejuni Simpl-Like Protein
ComponentsPeriplasmic protein
KeywordsMEMBRANE PROTEIN / Campylobacter jejuni / Simpl-Like Protein / SLP
Function / homologyUncharacterised conserved protein UCP029033, periplasmic protein / Interleukin-1 receptor-associated kinase 1-binding protein 1/DUF541 / : / Protein of unknown function (DUF541) / DNA damage response / Periplasmic protein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsGregor, W.D. / Zhang, Z. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145069 United States
CitationJournal: To Be Published
Title: C. Jejuni Simpl-Like Protein
Authors: Gregor, W.D. / Zhang, Z. / Yu, E.W.
History
DepositionJan 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 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

Downloads & links

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Assembly

Deposited unit
A: Periplasmic protein
B: Periplasmic protein
C: Periplasmic protein
D: Periplasmic protein
E: Periplasmic protein
F: Periplasmic protein
G: Periplasmic protein
H: Periplasmic protein
I: Periplasmic protein


Theoretical massNumber of molelcules
Total (without water)236,0419
Polymers236,0419
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
Periplasmic protein


Mass: 26226.803 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / References: UniProt: Q0PC92
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: Simpl-Like Protein / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
220 mMsodium chlorideNaCl1
SpecimenConc.: 10 mg/ml / Embedding 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: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 102032
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9242 / Symmetry type: POINT
RefinementHighest resolution: 3.13 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316839
ELECTRON MICROSCOPYf_angle_d0.40922734
ELECTRON MICROSCOPYf_dihedral_angle_d9.1666390
ELECTRON MICROSCOPYf_chiral_restr0.0432655
ELECTRON MICROSCOPYf_plane_restr0.0032898

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