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- EMDB-74167: 7118 Fab in complex with Plasmodium falciparum rsCSP -

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Basic information

Entry
Database: EMDB / ID: EMD-74167
Title7118 Fab in complex with Plasmodium falciparum rsCSP
Map data
Sample
  • Complex: 7118 Fab in complex with Plasmodium falciparum rsCSP
    • Protein or peptide: Fab 7118 Heavy Chain
    • Protein or peptide: Fab 7118 Light Chain
    • Protein or peptide: Circumsporozoite Protein
KeywordsPlasmodium / malaria / CSP / Fab / homotypic / IMMUNE SYSTEM
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCannac F / Lee WH / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-056202 United States
Bill & Melinda Gates FoundationIINV-004923 United States
CitationJournal: To Be Published
Title: Structural basis for conserved and distinct antigen recognition by a lineage of malaria-protective antibodies
Authors: Jain M / Cannac F
History
DepositionDec 2, 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_74167.png

Downloads & links

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Map

FileDownload / File: emd_74167.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 440 pix.
= 315.92 Å		0.72 Å/pix.
x 440 pix.
= 315.92 Å		0.72 Å/pix.
x 440 pix.
= 315.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.7743095 - 1.088583
Average (Standard dev.)-0.00018430686 (±0.014363925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 315.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74167_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74167_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_74167_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 : 7118 Fab in complex with Plasmodium falciparum rsCSP

EntireName: 7118 Fab in complex with Plasmodium falciparum rsCSP
Components
  • Complex: 7118 Fab in complex with Plasmodium falciparum rsCSP
    • Protein or peptide: Fab 7118 Heavy Chain
    • Protein or peptide: Fab 7118 Light Chain
    • Protein or peptide: Circumsporozoite Protein

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Supramolecule #1: 7118 Fab in complex with Plasmodium falciparum rsCSP

SupramoleculeName: 7118 Fab in complex with Plasmodium falciparum rsCSP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: Fab 7118 Heavy Chain

MacromoleculeName: Fab 7118 Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.34086 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQVVESGGG VVQPGRSLRL SCTASGFTFG DYAMSWFRQA PGKGLEWVGF IRSEANGGAP EYAASVKGRF TISRDDFKSI AYLQMNSLK TEDTAAYYCT RVRTNDFRDM DVWGKGTTVA VSS

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Macromolecule #2: Fab 7118 Light Chain

MacromoleculeName: Fab 7118 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.521192 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIVMTQTPLS LSVTPGQPAS ISCKSTESLL HRDGKTYLYW YLQKPGQPPQ LLIYEVSNRF SGVPDRFSGS GSVTDFTLKI SRVEAEDIG VYYCMQTIDL PWTFGQGTKV EIK

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Macromolecule #3: Circumsporozoite Protein

MacromoleculeName: Circumsporozoite Protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 30.232156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YGSSSNTRVL NELNYDNAGT NLYNELEMNY YGKQENWYSL KKNSRSLGEN DDGNNEDNEK LRKPKHKKLK QPADGNPDPN ANPNVDPNA NPNVDPNANP NVDPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP N ANPNANPN ...String:
YGSSSNTRVL NELNYDNAGT NLYNELEMNY YGKQENWYSL KKNSRSLGEN DDGNNEDNEK LRKPKHKKLK QPADGNPDPN ANPNVDPNA NPNVDPNANP NVDPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP N ANPNANPN KNNQGNGQGH NMPNDPNRNV DENANANSAV KNNNNEEPSD KHIKEYLNKI QNSLSTEWSP CSVTCGNGIQ VR IKPGSAN KPKDELDYAN DIEKKICKME KCSSVFNVVN S

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 2065 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 250774
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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