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- PDB-9oqd: Chlamydia muridarum major outer membrane protein bound to Mus mus... -

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Basic information

Entry
Database: PDB / ID: 9oqd
TitleChlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
Components
  • MAB-18B Fab heavy chain
  • MAB-18B Fab light chain
  • Major outer membrane porin
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / Chlamydia muridarum major outer membrane protein / porin / CHL vaccine candidate / MEMBRANE PROTEIN-IMMUNE SYSTEM complex / STRUCTURAL GENOMICS / CSBID / Center for Structural Biology of Infectious Diseases
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane / regulation of cell shape / structural molecule activity
Similarity search - Function
Major outer membrane protein, Chlamydia / Chlamydia major outer membrane protein
Similarity search - Domain/homology
LAURIC ACID / sphingomyelin / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Major outer membrane porin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Chlamydia muridarum (agent of mouse pneumonitis)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsGuo, Y. / Borek, D. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Chlamydia Muridarum Major Outer Membrane Protein Bound To Mus Musculus Mab-18B Fab
Authors: Guo, Y. / Borek, D. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionMay 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / 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: MAB-18B Fab light chain
B: MAB-18B Fab heavy chain
C: Major outer membrane porin
D: MAB-18B Fab light chain
E: MAB-18B Fab heavy chain
F: Major outer membrane porin
G: MAB-18B Fab light chain
H: MAB-18B Fab heavy chain
I: Major outer membrane porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,86924
Polymers261,9939
Non-polymers5,87615
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.5, -0.866025), (0.866025, -0.5), (1)510.58823, 136.81177
3given(-0.5, 0.866025), (-0.866025, -0.5), (1)136.81178, 510.58825

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Components

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Antibody , 2 types, 6 molecules ADGBEH

#1: Antibody MAB-18B Fab light chain


Mass: 24084.834 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody MAB-18B Fab heavy chain


Mass: 23456.316 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein / Sugars , 2 types, 6 molecules CFI

#3: Protein Major outer membrane porin / MOMP


Mass: 39789.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chlamydia muridarum (agent of mouse pneumonitis)
References: UniProt: P75024
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 12 molecules

#4: Chemical ChemComp-PEX / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 522.632 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H49NO8P
#5: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical ChemComp-FO4 / sphingomyelin


Mass: 814.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H94N2O6P

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Details

Has ligand of interestN
Has protein modificationY

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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: Chlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Chlamydia muridarum (agent of mouse pneumonitis)
Buffer solutionpH: 5.5
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: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51710 / Symmetry type: POINT
RefinementHighest resolution: 3.36 Å

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