[English] 日本語
Yorodumi
- EMDB-20444: Fab667 in complex with recombinant, shortened circumsporozoite protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20444
TitleFab667 in complex with recombinant, shortened circumsporozoite protein
Map dataFab667 in complex with recombinant, shortened circumsporozoite protein.
Sample
  • Complex: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 667
    • Complex: fragment antigen binding (fab) 667
    • Complex: recombinant, shortened circumsporozoite protein
Biological speciesHomo sapiens (human) / Plasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsTorres JL / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: PLoS Pathog / Year: 2020
Title: Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein.
Authors: David Oyen / Jonathan L Torres / Phillip C Aoto / Yevel Flores-Garcia / Špela Binter / Tossapol Pholcharee / Sean Carroll / Sini Reponen / Rachael Wash / Qi Liang / Franck Lemiale / Emily ...Authors: David Oyen / Jonathan L Torres / Phillip C Aoto / Yevel Flores-Garcia / Špela Binter / Tossapol Pholcharee / Sean Carroll / Sini Reponen / Rachael Wash / Qi Liang / Franck Lemiale / Emily Locke / Allan Bradley / C Richter King / Daniel Emerling / Paul Kellam / Fidel Zavala / Andrew B Ward / Ian A Wilson /
Abstract: Lasting protection has long been a goal for malaria vaccines. The major surface antigen on Plasmodium falciparum sporozoites, the circumsporozoite protein (PfCSP), has been an attractive target for ...Lasting protection has long been a goal for malaria vaccines. The major surface antigen on Plasmodium falciparum sporozoites, the circumsporozoite protein (PfCSP), has been an attractive target for vaccine development and most protective antibodies studied to date interact with the central NANP repeat region of PfCSP. However, it remains unclear what structural and functional characteristics correlate with better protection by one antibody over another. Binding to the junctional region between the N-terminal domain and central NANP repeats has been proposed to result in superior protection: this region initiates with the only NPDP sequence followed immediately by NANP. Here, we isolated antibodies in Kymab mice immunized with full-length recombinant PfCSP and two protective antibodies were selected for further study with reactivity against the junctional region. X-ray and EM structures of two monoclonal antibodies, mAb667 and mAb668, shed light on their differential affinity and specificity for the junctional region. Importantly, these antibodies also bind to the NANP repeat region with equal or better affinity. A comparison with an NANP-only binding antibody (mAb317) revealed roughly similar but statistically distinct levels of protection against sporozoite challenge in mouse liver burden models, suggesting that junctional antibody protection might relate to the ability to also cross-react with the NANP repeat region. Our findings indicate that additional efforts are necessary to isolate a true junctional antibody with no or much reduced affinity to the NANP region to elucidate the role of the junctional epitope in protection.
History
DepositionJul 8, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseApr 8, 2020-
UpdateApr 8, 2020-
Current statusApr 8, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.32
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20444.png

Downloads & links

-
Map

FileDownload / File: emd_20444.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFab667 in complex with recombinant, shortened circumsporozoite protein.
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: 1.32 / Movie #1: 1.32
Minimum - Maximum-0.38547587 - 4.892455
Average (Standard dev.)0.03182782 (±0.22098067)
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-0.3854.8920.032

-
Supplemental data

-
Sample components

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

EntireName: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 667
Components
  • Complex: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 667
    • Complex: fragment antigen binding (fab) 667
    • Complex: recombinant, shortened circumsporozoite protein

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

SupramoleculeName: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 667
type: complex / ID: 1 / Parent: 0
Molecular weightExperimental: 500 KDa

-
Supramolecule #2: fragment antigen binding (fab) 667

SupramoleculeName: fragment antigen binding (fab) 667 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Supramolecule #3: recombinant, shortened circumsporozoite protein

SupramoleculeName: recombinant, shortened circumsporozoite protein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 (w/v)
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CELLULOSE ACETATE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER

-
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 opticsCalibrated 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

+
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: ab-initio in cryosparc 2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 15980
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

+
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