[English] 日本語
Yorodumi
- PDB-8qu7: Crystal structure of the Plasmodium falciparum Apical membrane an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qu7
TitleCrystal structure of the Plasmodium falciparum Apical membrane antigen (AMA1) in complex with single domain i-body WD34
Components
  • Apical membrane antigen 1
  • single domain i-body WD34
KeywordsPROTEIN BINDING / Plasmodium / AMA1 / i-body
Function / homologyApical membrane antigen 1 domain superfamily / adhesion of symbiont to host cell / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane / Apical membrane antigen 1
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Citation
Journal: Nat Commun / Year: 2024
Title: A broadly cross-reactive i-body to AMA1 potently inhibits blood and liver stages of Plasmodium parasites.
Authors: Angage, D. / Chmielewski, J. / Maddumage, J.C. / Hesping, E. / Caiazzo, S. / Lai, K.H. / Yeoh, L.M. / Menassa, J. / Opi, D.H. / Cairns, C. / Puthalakath, H. / Beeson, J.G. / Kvansakul, M. / ...Authors: Angage, D. / Chmielewski, J. / Maddumage, J.C. / Hesping, E. / Caiazzo, S. / Lai, K.H. / Yeoh, L.M. / Menassa, J. / Opi, D.H. / Cairns, C. / Puthalakath, H. / Beeson, J.G. / Kvansakul, M. / Boddey, J.A. / Wilson, D.W. / Anders, R.F. / Foley, M.
#1: Journal: Res Sq / Year: 2024
Title: A broadly cross-reactive i-body to AMA1 potently inhibits blood and liver stages of Plasmodium parasites
Authors: Foley, M. / Angage, D. / Anders, R. / Chmielewski, J. / Maddumage, J.C. / Hesping, E. / Caiazzo, S. / Lai, K.H. / Yeoh, L. / Opi, H. / Cairns, C. / Beeson, J. / Kvansakul, M. / Wilson, D. / Boddey, J.
History
DepositionOct 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Apical membrane antigen 1
A: single domain i-body WD34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6455
Polymers55,2662
Non-polymers3793
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-23 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.651, 38.462, 227.355
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

-
Protein , 2 types, 2 molecules EA

#1: Protein Apical membrane antigen 1 / Merozoite surface antigen


Mass: 41462.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: AMA-1, PF83 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P22621
#2: Protein single domain i-body WD34


Mass: 13803.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)

-
Non-polymers , 4 types, 68 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1MSodium HEPES pH7.5 70% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.6→38.45 Å / Num. obs: 19822 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.06 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 2335 / CC1/2: 0.864

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.45 Å / SU ML: 0.261 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1010 5.15 %
Rwork0.2132 18598 -
obs0.2143 19608 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 24 65 2994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282997
X-RAY DIFFRACTIONf_angle_d0.60294079
X-RAY DIFFRACTIONf_chiral_restr0.0448446
X-RAY DIFFRACTIONf_plane_restr0.005530
X-RAY DIFFRACTIONf_dihedral_angle_d12.86421075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.26341220.24872671X-RAY DIFFRACTION99.93
2.74-2.910.31081470.2472595X-RAY DIFFRACTION100
2.91-3.130.25691500.2362617X-RAY DIFFRACTION99.82
3.13-3.450.23581190.20612661X-RAY DIFFRACTION99.93
3.45-3.950.20391630.19622620X-RAY DIFFRACTION99.96
3.95-4.970.19561480.18062672X-RAY DIFFRACTION99.89
4.97-38.450.25321610.22982762X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -31.0160550045 Å / Origin y: -6.6041637606 Å / Origin z: -40.7436801463 Å
111213212223313233
T0.260880556551 Å20.0146250334475 Å20.0271787532271 Å2-0.26588220804 Å2-0.0100537422245 Å2--0.331682356707 Å2
L1.93265769579 °2-0.333190331649 °20.537488285235 °2-1.10100701922 °2-0.263667545032 °2--1.28120084285 °2
S-0.0381927189974 Å °-0.342292420291 Å °0.00607039452183 Å °0.24587764691 Å °0.0408655808053 Å °-0.0496212038567 Å °-0.0203007971813 Å °0.0499983219918 Å °-0.00913683813334 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