[English] 日本語
Yorodumi
- PDB-8gie: Crystal structure of a designed single-component Plasmodium falci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gie
TitleCrystal structure of a designed single-component Plasmodium falciparum AMA1-RON2L insertion fusion immunogen 2
ComponentsApical membrane antigen 1, rhoptry neck protein 2 chimera
KeywordsCELL INVASION / Single component immunogens / Malaria vaccines
Function / homology
Function and homology information


rhoptry neck / apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Domain/homology
Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPatel, P.N. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001253 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure-based design of a strain transcending AMA1-RON2L malaria vaccine.
Authors: Patel, P.N. / Dickey, T.H. / Diouf, A. / Salinas, N.D. / McAleese, H. / Ouahes, T. / Long, C.A. / Miura, K. / Lambert, L.E. / Tolia, N.H.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apical membrane antigen 1, rhoptry neck protein 2 chimera


Theoretical massNumber of molelcules
Total (without water)38,5871
Polymers38,5871
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.630, 62.830, 60.470
Angle α, β, γ (deg.)90.000, 96.470, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Apical membrane antigen 1, rhoptry neck protein 2 chimera / Merozoite surface antigen


Mass: 38587.023 Da / Num. of mol.: 1 / Mutation: T64A,T225A,S325A,S326A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1133400, PF3D7_1452000 / Plasmid: pHL-sec / Cell (production host): 293-derived Cells / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q7KQK5, UniProt: Q8IKV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 M Lithium Chloride, 0.1 M Tris (pH 8.5), 34% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→19.22 Å / Num. obs: 25370 / % possible obs: 97.67 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.65 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.0998 / Rpim(I) all: 0.0638 / Rrim(I) all: 0.1189 / Net I/σ(I): 10.61
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.6761 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 2516 / CC1/2: 0.994 / CC star: 0.924 / Rpim(I) all: 0.4264 / Rrim(I) all: 0.1189 / % possible all: 97.52

-
Processing

Software
NameVersionClassification
SERGUIdata collection
XDSv Jan 10, 2022data reduction
XSCALEv Jan 10, 2022data scaling
PHENIX1.20.1_4487phasing
Coot0.9model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.22 Å / SU ML: 0.2491 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 1269 5 %
Rwork0.1914 24101 -
obs0.1925 25370 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 0 109 2516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352467
X-RAY DIFFRACTIONf_angle_d0.62583347
X-RAY DIFFRACTIONf_chiral_restr0.045355
X-RAY DIFFRACTIONf_plane_restr0.0063442
X-RAY DIFFRACTIONf_dihedral_angle_d11.6181907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.39441390.37152645X-RAY DIFFRACTION97.62
1.92-2.010.26551420.23922698X-RAY DIFFRACTION99.06
2.01-2.120.25851420.19982688X-RAY DIFFRACTION98.85
2.12-2.250.24141380.19842625X-RAY DIFFRACTION95.44
2.25-2.420.18951420.17792708X-RAY DIFFRACTION99.37
2.42-2.660.20251430.18352709X-RAY DIFFRACTION98.72
2.66-3.050.24461400.19292668X-RAY DIFFRACTION97.84
3.05-3.830.1971400.17822651X-RAY DIFFRACTION95.71
3.84-19.220.1811430.17992709X-RAY DIFFRACTION96.61
Refinement TLS params.Method: refined / Origin x: 11.8928084914 Å / Origin y: 10.7228847087 Å / Origin z: 4.83376803442 Å
111213212223313233
T0.118459712978 Å20.000710846209782 Å2-0.0172925117133 Å2-0.114699777508 Å20.0117509189568 Å2--0.213308416114 Å2
L0.746015590092 °2-0.163468412404 °2-0.925425530358 °2-0.688653809412 °20.431270532567 °2--3.79542319046 °2
S0.0100619411553 Å °-0.00324329538829 Å °0.0482121864178 Å °0.0251606370223 Å °0.00632924434496 Å °-0.00382826276346 Å °-0.00927950842333 Å °-0.060997744033 Å °-0.00721076869814 Å °
Refinement TLS groupSelection details: all

+
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