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- EMDB-45640: L9 epitope scaffold complexed with L9 Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-45640
TitleL9 epitope scaffold complexed with L9 Fabs
Map data
Sample
  • Complex: L9 epitope scaffold complexed with L9 fabs
    • Protein or peptide: L9 epitope Scaffold
    • Protein or peptide: L9 heavy chain
    • Protein or peptide: L9 light chain
KeywordsMalaria / Scaffold / PfCSP / Antibody / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Plasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRaghavan SSR / Lee WH / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: Scaffolding disordered repeat epitopes of Plasmodium falciparum circumsporozoite by combined machine learning approaches
Authors: Raghavan SSR / Lee WH / Ward AB
History
DepositionJul 8, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45640.png

Downloads & links

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Map

FileDownload / File: emd_45640.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: 0.23
Minimum - Maximum-1.1199279 - 1.605981
Average (Standard dev.)-0.00028107176 (±0.018887112)
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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Additional map: #1

Fileemd_45640_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45640_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_45640_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 : L9 epitope scaffold complexed with L9 fabs

EntireName: L9 epitope scaffold complexed with L9 fabs
Components
  • Complex: L9 epitope scaffold complexed with L9 fabs
    • Protein or peptide: L9 epitope Scaffold
    • Protein or peptide: L9 heavy chain
    • Protein or peptide: L9 light chain

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Supramolecule #1: L9 epitope scaffold complexed with L9 fabs

SupramoleculeName: L9 epitope scaffold complexed with L9 fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: L9 epitope Scaffold

MacromoleculeName: L9 epitope Scaffold / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 11.231568 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MKESFNAKIT IYENPNVNGR VEEFEGKITK VSEDTYEITV KRNPNVPDEK YTVKGKEEKL EDGNTLITGK LTGTNPNVVV NADIIVKKT DGTKHHHHHH

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Macromolecule #2: L9 heavy chain

MacromoleculeName: L9 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.336896 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVKLVESGGG VVQPGRSLRL SCEASGFIFS TYGMHWVRQA PGKGLEWVAV IWFDGSNIYY ADSVKGRFTI SRDNSKNTVF MQMDSLRAE DTAVYYCHRN FYDGSGPFDY WGQGTLVTVS

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Macromolecule #3: L9 light chain

MacromoleculeName: L9 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: Cricetulus griseus (Chinese hamster)
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

Concentration0.1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 370307
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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