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- EMDB-72924: Cryo-EM structure of L9-F4 in complex with Plasmodium falciparum ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72924
TitleCryo-EM structure of L9-F4 in complex with Plasmodium falciparum circumsporozoite protein (PfCSP)
Map data
Sample
  • Complex: PfCSP:L9-F4
    • Protein or peptide: Circumsporozoite protein
    • Protein or peptide: L9-F4 heavy chain
    • Protein or peptide: L9-F4 light chain
KeywordsAnti-Malarial / PfCSP / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
: / Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesPlasmodium falciparum (isolate 3D7) (eukaryote) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsTripathi P / Kwong PD
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: Cryo-EM structure of L9-F4 in complex with Plasmodium falciparum circumsporozoite protein (PfCSP)
Authors: Tripathi P / Kwong PD
History
DepositionSep 28, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72924.png

Downloads & links

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Map

FileDownload / File: emd_72924.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.)
0.92 Å/pix.
x 320 pix.
= 294.08 Å		0.92 Å/pix.
x 320 pix.
= 294.08 Å		0.92 Å/pix.
x 320 pix.
= 294.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.919 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.473
Minimum - Maximum-2.4054358 - 3.4219756
Average (Standard dev.)-0.00074899173 (±0.064377606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 294.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EMready modified map

Fileemd_72924_additional_1.map
AnnotationEMready modified map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72924_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_72924_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 : PfCSP:L9-F4

EntireName: PfCSP:L9-F4
Components
  • Complex: PfCSP:L9-F4
    • Protein or peptide: Circumsporozoite protein
    • Protein or peptide: L9-F4 heavy chain
    • Protein or peptide: L9-F4 light chain

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Supramolecule #1: PfCSP:L9-F4

SupramoleculeName: PfCSP:L9-F4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote)

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Macromolecule #1: Circumsporozoite protein

MacromoleculeName: Circumsporozoite protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote)
Molecular weightTheoretical: 42.676547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMRKLAILSV SSFLFVEALF QEYQCYGSSS NTRVLNELNY DNAGTNLYNE LEMNYYGKQE NWYSLKKNSR SLGENDDGNN EDNEKLRKP KHKKLKQPAD GNPDPNANPN VDPNANPNVD PNANPNVDPN ANPNANPNAN PNANPNANPN ANPNANPNAN P NANPNANP ...String:
MMRKLAILSV SSFLFVEALF QEYQCYGSSS NTRVLNELNY DNAGTNLYNE LEMNYYGKQE NWYSLKKNSR SLGENDDGNN EDNEKLRKP KHKKLKQPAD GNPDPNANPN VDPNANPNVD PNANPNVDPN ANPNANPNAN PNANPNANPN ANPNANPNAN P NANPNANP NANPNANPNA NPNANPNANP NANPNANPNV DPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NP NANPNAN PNANPNANPN ANPNANPNAN PNANPNKNNQ GNGQGHNMPN DPNRNVDENA NANSAVKNNN NEEPSDKHIK EYL NKIQNS LSTEWSPCSV TCGNGIQVRI KPGSANKPKD ELDYANDIEK KICKMEKCSS VFNVVNSSIG LIMVLSFLFL N

UniProtKB: Circumsporozoite protein

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Macromolecule #2: L9-F4 heavy chain

MacromoleculeName: L9-F4 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.400962 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVKLVESGGG VVQPGRSLRL SCEASGFIFS TYGIHWVRQA PGKGLEWVAV IWFDGSNIYY ADSVKGRFTI SRDNSKNTVF LQMDSLRAE DTAVYYCHRN FYDRSGPFDY WGQGTLVTVS

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Macromolecule #3: L9-F4 light chain

MacromoleculeName: L9-F4 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.837231 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQFIS RWLAWYQQKP GKAPKLLIYK ASSLESGVPS RFSGSGSETH FTLTISSLQP DDVATYYCQ EYTSYGRTFG QGTKVEIK

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: OTHER / Average electron dose: 56.36 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8ek1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82521
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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