[English] 日本語
Yorodumi
- EMDB-7068: rsCSP + Fab311 Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7068
TitlersCSP + Fab311 Complex
Map datarsCSP + Fab311 Complex
Sample
  • Complex: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 311
    • Complex: Complex containing recombinant, shortened circumsporozite protein (CSP)
    • Complex: Fragment antigen binding (Fab) 311
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTorres JL / Ward AB
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural basis for antibody recognition of the NANP repeats in circumsporozoite protein.
Authors: David Oyen / Jonathan L Torres / Ulrike Wille-Reece / Christian F Ockenhouse / Daniel Emerling / Jacob Glanville / Wayne Volkmuth / Yevel Flores-Garcia / Fidel Zavala / Andrew B Ward / C ...Authors: David Oyen / Jonathan L Torres / Ulrike Wille-Reece / Christian F Ockenhouse / Daniel Emerling / Jacob Glanville / Wayne Volkmuth / Yevel Flores-Garcia / Fidel Zavala / Andrew B Ward / C Richter King / Ian A Wilson /
Abstract: Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)- ...Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)-based vaccine against that contains 19 NANP repeats followed by a thrombospondin repeat domain. Although RTS,S has undergone extensive clinical testing and has progressed through phase III clinical trials, continued efforts are underway to enhance its efficacy and duration of protection. Here, we determined that two monoclonal antibodies (mAbs 311 and 317), isolated from a recent controlled human malaria infection trial exploring a delayed fractional dose, inhibit parasite development in vivo by at least 97%. Crystal structures of antibody fragments (Fabs) 311 and 317 with an (NPNA) peptide illustrate their different binding modes. Notwithstanding, one and three of the three NPNA repeats adopt similar well-defined type I β-turns with Fab311 and Fab317, respectively. Furthermore, to explore antibody binding in the context of CSP, we used negative-stain electron microscopy on a recombinant shortened CSP (rsCSP) construct saturated with Fabs. Both complexes display a compact rsCSP with multiple Fabs bound, with the rsCSP-Fab311 complex forming a highly organized helical structure. Together, these structural insights may aid in the design of a next-generation malaria vaccine.
History
DepositionOct 9, 2017-
Header (metadata) releaseNov 1, 2017-
Map releaseNov 15, 2017-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0228
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0228
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7068.png

Downloads & links

-
Map

FileDownload / File: emd_7068.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationrsCSP + Fab311 Complex
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 0.0228 / Movie #1: 0.0228
Minimum - Maximum-0.06592668 - 0.06665512
Average (Standard dev.)-0.0000916984 (±0.005521115)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0660.067-0.000

-
Supplemental data

-
Sample components

-
Entire : Complex containing recombinant, shortened circumsporozite protein...

EntireName: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 311
Components
  • Complex: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 311
    • Complex: Complex containing recombinant, shortened circumsporozite protein (CSP)
    • Complex: Fragment antigen binding (Fab) 311

-
Supramolecule #1: Complex containing recombinant, shortened circumsporozite protein...

SupramoleculeName: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 311
type: complex / ID: 1 / Parent: 0
Details: Plasmodium falciparum's circumsporozite protein in complex with Fab311, a protecting antibody from the RTS,S clinical trial

-
Supramolecule #2: Complex containing recombinant, shortened circumsporozite protein...

SupramoleculeName: Complex containing recombinant, shortened circumsporozite protein (CSP)
type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 492 KDa

-
Supramolecule #3: Fragment antigen binding (Fab) 311

SupramoleculeName: Fragment antigen binding (Fab) 311 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
50.0 mM(HOCH2)3CNH2Tris
StainingType: NEGATIVE / Material: 2% (w/v) Uranyl Formate
Details: add 3 uL sample, blot, add 3 uL 2% uranyl formate, blot immediately, add 3 uL 2% uranyl formate, blot after 30 seconds
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CELLULOSE ACETATE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Details: 15 mA

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 6320
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 20
Software - Name: EMAN (ver. 2) / Software - details: e2initialmodel.py / Details: Used EMAN2 e2initialmodel
Final 3D classificationNumber classes: 3 / Avg.num./class: 7000 / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 6320

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more