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- EMDB-20772: Fab397 in complex with NPNA8 peptide (Class 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-20772
TitleFab397 in complex with NPNA8 peptide (Class 1)
Map dataFab397 in complex with NPNA8 peptide (Class 1)
Sample
  • Complex: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide (Class 1)
    • Complex: fragment antigen binding (fab) 397
    • Complex: NPNA8 Peptide
Biological speciesHomo sapiens (human) / Plasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsWard AB / Torres JL
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: J Mol Biol / Year: 2020
Title: Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein.
Authors: Tossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / ...Authors: Tossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / Fidel Zavala / Andrew B Ward / Ian A Wilson /
Abstract: Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 ...Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This "conserved" Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding.
History
DepositionSep 27, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseJan 15, 2020-
UpdateMar 11, 2020-
Current statusMar 11, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20772.png

Downloads & links

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Map

FileDownload / File: emd_20772.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFab397 in complex with NPNA8 peptide (Class 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.35 / Movie #1: 1.35
Minimum - Maximum-0.57209 - 3.9215696
Average (Standard dev.)0.0062596286 (±0.17536926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.5723.9220.006

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Supplemental data

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Sample components

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Entire : Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide ...

EntireName: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide (Class 1)
Components
  • Complex: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide (Class 1)
    • Complex: fragment antigen binding (fab) 397
    • Complex: NPNA8 Peptide

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Supramolecule #1: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide ...

SupramoleculeName: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide (Class 1)
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: fragment antigen binding (fab) 397

SupramoleculeName: fragment antigen binding (fab) 397 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: NPNA8 Peptide

SupramoleculeName: NPNA8 Peptide / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mM(HOCH2)3CNH2Tris
150.0 mMNaClsodium chloride
StainingType: NEGATIVE / Material: 2% Uranyl Formate
GridModel: Homemade / Material: COPPER / Support film - Material: CELLULOSE ACETATE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 10875
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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