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- EMDB-70746: Chlamydia muridarum major outer membrane protein bound to Mus mus... -

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Basic information

Entry
Database: EMDB / ID: EMD-70746
TitleChlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
Map data
Sample
  • Complex: Chlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
    • Protein or peptide: MAB-18B Fab light chain
    • Protein or peptide: MAB-18B Fab heavy chain
    • Protein or peptide: Major outer membrane porin
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: LAURIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: sphingomyelin
KeywordsChlamydia 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 / homologyMajor outer membrane protein, Chlamydia / Chlamydia major outer membrane protein / porin activity / pore complex / monoatomic ion transport / cell outer membrane / regulation of cell shape / structural molecule activity / Major outer membrane porin
Function and homology information
Biological speciesChlamydia muridarum (agent of mouse pneumonitis) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsGuo Y / Borek D / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70746.png

Downloads & links

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Map

FileDownload / File: emd_70746.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 431.6 Å		1.08 Å/pix.
x 400 pix.
= 431.6 Å		1.08 Å/pix.
x 400 pix.
= 431.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.29244843 - 0.5812917
Average (Standard dev.)0.00049815286 (±0.012179344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 431.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70746_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_70746_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 : Chlamydia muridarum major outer membrane protein bound to Mus mus...

EntireName: Chlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
Components
  • Complex: Chlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
    • Protein or peptide: MAB-18B Fab light chain
    • Protein or peptide: MAB-18B Fab heavy chain
    • Protein or peptide: Major outer membrane porin
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: LAURIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: sphingomyelin

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Supramolecule #1: Chlamydia muridarum major outer membrane protein bound to Mus mus...

SupramoleculeName: Chlamydia muridarum major outer membrane protein bound to Mus musculus MAB-18B Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Chlamydia muridarum (agent of mouse pneumonitis)

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Macromolecule #1: MAB-18B Fab light chain

MacromoleculeName: MAB-18B Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.084834 KDa
SequenceString: DIVMTQAAPS VPVTPGESVS ISCRSSKSLL HSNGNTYLYW FLQRPGQSPQ LLIYRMSNLA SGVPDRFSGS GSGTAFILRI SRVEAEDVG VYYCMQHLEY PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DIVMTQAAPS VPVTPGESVS ISCRSSKSLL HSNGNTYLYW FLQRPGQSPQ LLIYRMSNLA SGVPDRFSGS GSGTAFILRI SRVEAEDVG VYYCMQHLEY PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE

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Macromolecule #2: MAB-18B Fab heavy chain

MacromoleculeName: MAB-18B Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.456316 KDa
SequenceString: QVQLQQSGPE LVRPGVSVKI SCKGSGYTFT DYSMHWVKQS HAKSLEWIGV ISPYSGNTKY NQKFKDKATM TVDKSSSTAF MELARLTSE DSAIFYCARG ITTGYYAMDY WGQGTSVTVS SAKTTPPSVY PLAPGCGDTT GSSVTLGCLV KGYFPEPVTV T WNSGSLSS ...String:
QVQLQQSGPE LVRPGVSVKI SCKGSGYTFT DYSMHWVKQS HAKSLEWIGV ISPYSGNTKY NQKFKDKATM TVDKSSSTAF MELARLTSE DSAIFYCARG ITTGYYAMDY WGQGTSVTVS SAKTTPPSVY PLAPGCGDTT GSSVTLGCLV KGYFPEPVTV T WNSGSLSS SVHTFPALLQ SGLYTMSSSV TVPSSTWPSQ TVTCSVAHPA SSTTVDKKLE P

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Macromolecule #3: Major outer membrane porin

MacromoleculeName: Major outer membrane porin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chlamydia muridarum (agent of mouse pneumonitis)
Molecular weightTheoretical: 39.789793 KDa
SequenceString: LPVGNPAEPS LMIDGILWEG FGGDPCDPCT TWCDAISLRL GYYGDFVFDR VLKTDVNKQF EMGAAPTGDA DLTTAPTPAS RENPAYGKH MQDAEMFTNA AYMALNIWDR FDVFCTLGAT SGYLKGNSAA FNLVGLFGRD ETAVAADDIP NVSLSQAVVE L YTDTAFAW ...String:
LPVGNPAEPS LMIDGILWEG FGGDPCDPCT TWCDAISLRL GYYGDFVFDR VLKTDVNKQF EMGAAPTGDA DLTTAPTPAS RENPAYGKH MQDAEMFTNA AYMALNIWDR FDVFCTLGAT SGYLKGNSAA FNLVGLFGRD ETAVAADDIP NVSLSQAVVE L YTDTAFAW SVGARAALWE CGCATLGASF QYAQSKPKVE ELNVLCNAAE FTINKPKGYV GQEFPLNIKA GTVSATDTKD AS IDYHEWQ ASLALSYRLN MFTPYIGVKW SRASFDADTI RIAQPKLETS ILKMTTWNPT ISGSGIDVDT KITDTLQIVS LQL NKMKSR KSCGLAIGTT IVDADKYAVT VETRLIDERA AHVNAQFRF

UniProtKB: Major outer membrane porin

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Macromolecule #4: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 4 / Number of copies: 3 / Formula: PEX
Molecular weightTheoretical: 522.632 Da
Chemical component information

ChemComp-PEX:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

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Macromolecule #5: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 5 / Number of copies: 6 / Formula: DAO
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: sphingomyelin

MacromoleculeName: sphingomyelin / type: ligand / ID: 7 / Number of copies: 3 / Formula: FO4
Molecular weightTheoretical: 814.233 Da
Chemical component information

ChemComp-FO4:
sphingomyelin

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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: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51710
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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