[English] 日本語
Yorodumi
- PDB-9n5i: Endogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n5i
TitleEndogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Components
  • (Gametocyte surface protein ...) x 2
  • RUPA-44 Fab heavy chain
  • RUPA-44 Fab kappa chain
  • RUPA-71 Fab heavy chain
  • RUPA-71 Fab kappa chain
KeywordsIMMUNE SYSTEM / Pfs48/45 / Pfs230 / Malaria / transmission-blocking antibodies
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
Gametocyte surface protein P230 / Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsHailemariam, S. / Heide, F. / Bekkering, E. / Ivanochko, D. / Yoo, R. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Immunity / Year: 2025
Title: Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity
Authors: Bekkering, E. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O. / van Daalen, R. ...Authors: Bekkering, E. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O. / van Daalen, R. / Inklaar, M. / Andrade, C. / Jansen, P. / Vermeulen, M. / Bousema, T. / Takashima, E. / Rubinstein, J. / Kooij, T. / Jore, M. / Julien, J.P.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gametocyte surface protein P230
D: Gametocyte surface protein P45/48
E: RUPA-44 Fab kappa chain
F: RUPA-44 Fab heavy chain
H: RUPA-71 Fab heavy chain
L: RUPA-71 Fab kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,6857
Polymers511,3186
Non-polymers3671
Water00
1


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

-
Components

-
Gametocyte surface protein ... , 2 types, 2 molecules AD

#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 (malaria parasite P. falciparum)
References: UniProt: P68874
#2: Protein Gametocyte surface protein P45/48


Mass: 51545.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8I6T1

-
Antibody , 4 types, 4 molecules EFHL

#3: Antibody RUPA-44 Fab kappa chain


Mass: 23483.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 F / Production host: Homo sapiens (human)
#4: Antibody RUPA-44 Fab heavy chain


Mass: 24277.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 F / Production host: Homo sapiens (human)
#5: Antibody RUPA-71 Fab heavy chain


Mass: 24711.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#6: Antibody RUPA-71 Fab kappa chain


Mass: 23598.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

-
Sugars , 1 types, 1 molecules

#7: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Endogenous Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic 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: TFS FALCON 4i (4k x 4k)
Details: Images were collected at average electron doses per image of 50 and 53.7 electrons per square Angstrom 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
9cryoSPARCv4.6.0initial Euler assignment
10cryoSPARCv4.6.0final Euler assignment
11cryoSPARCv4.6.0classification
12cryoSPARCv4.6.03D reconstruction
13PHENIX1.21.1_5286model refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146814 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18U1P

8u1p

18U1P1PDBexperimental model
27UXL

7uxl

17UXL2PDBexperimental model
39N7K

9n7k

19N7K3PDBexperimental model
41AlphaFoldin silico model
RefinementHighest resolution: 3.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039451
ELECTRON MICROSCOPYf_angle_d0.52912816
ELECTRON MICROSCOPYf_dihedral_angle_d4.8831292
ELECTRON MICROSCOPYf_chiral_restr0.0461418
ELECTRON MICROSCOPYf_plane_restr0.0041627

+
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