[English] 日本語
Yorodumi
- PDB-9n5o: Endogenous Pfs230D7-8 in complex with 18F25 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n5o
TitleEndogenous Pfs230D7-8 in complex with 18F25
Components
  • 18F25 Heavy Chain
  • 18F25 Kappa Chain
  • Gametocyte surface protein P230
KeywordsIMMUNE SYSTEM / 6-Cys / antibody
Function / homology: / 6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesMus musculus (house mouse)
Plasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsJackman, J.J. / Yoo, R. / Ivanochko, D. / Hailemariam, S. / Bekkering, E. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Immunity / Year: 2025
Title: Structure of endogenous Pfs230:Pfs48/45 in complex with potent malaria transmission-blocking antibodies.
Authors: Bekkering, E.T. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van ...Authors: Bekkering, E.T. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van Daalen, R.C. / Inklaar, M.R. / Andrade, C.M. / Jansen, P.W.T.C. / Vermeulen, M. / Bousema, T. / Takashima, E. / Rubinstein, J.L. / Kooij, T.W.A. / Jore, M.M. / Julien, J.P.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Gametocyte surface protein P230
H: 18F25 Heavy Chain
L: 18F25 Kappa Chain


Theoretical massNumber of molelcules
Total (without water)410,7353
Polymers410,7353
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Gametocyte surface protein P230


Mass: 363701.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P68874
#2: Antibody 18F25 Heavy Chain


Mass: 23503.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody 18F25 Kappa Chain


Mass: 23530.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Endogenous Pfs230D7-8 in complex with 18F25 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMpotassium chlorideKCl1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K
Details: The Leica Automatic Plunge Freezer EM GP2 was used for freezing.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.5 sec. / Electron dose: 52 e/Å2 / Film or detector model: OTHER
Details: The Falcon 4i Direct Electron Detector was used. Images were collected at average electron doses per image of 50 and 53.7 during two data collections.
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.0particle selection
2EPUimage acquisition
4cryoSPARCv4.6.0CTF correction
7UCSF ChimeraX1.9model fitting
12cryoSPARCv4.6.03D reconstruction
19PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137749 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDDetailsSource nameTypeAccession code
11model generated in-houseAlphaFoldin silico model
29N6U

9n6u

1PDBexperimental model9N6U
RefinementHighest resolution: 4.32 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0084529
ELECTRON MICROSCOPYf_angle_d1.1136123
ELECTRON MICROSCOPYf_dihedral_angle_d10.7491684
ELECTRON MICROSCOPYf_chiral_restr0.055673
ELECTRON MICROSCOPYf_plane_restr0.007788

+
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