[English] 日本語
Yorodumi
- PDB-7pi7: PfCyRPA bound to monoclonal antibody Cy.002 Fab fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pi7
TitlePfCyRPA bound to monoclonal antibody Cy.002 Fab fragment
Components
  • Cysteine-rich protective antigen
  • Monoclonal antibody Cy.002 heavy chain
  • Monoclonal antibody Cy.002 light chain
KeywordsIMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
Cysteine-rich protective antigen 6 bladed domain / Cysteine-Rich Protective Antigen 6 bladed domain
Similarity search - Domain/homology
Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsRagotte, R.J. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
CitationJournal: Nat Commun / Year: 2022
Title: Heterotypic interactions drive antibody synergy against a malaria vaccine candidate.
Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / ...Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / Bowyer, P.W. / Higgins, M.K. / Draper, S.J.
History
DepositionAug 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.002 heavy chain
C: Monoclonal antibody Cy.002 light chain
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.002 heavy chain
F: Monoclonal antibody Cy.002 light chain


Theoretical massNumber of molelcules
Total (without water)174,7996
Polymers174,7996
Non-polymers00
Water1,36976
1
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.002 heavy chain
C: Monoclonal antibody Cy.002 light chain


Theoretical massNumber of molelcules
Total (without water)87,3993
Polymers87,3993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-30 kcal/mol
Surface area32600 Å2
MethodPISA
2
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.002 heavy chain
F: Monoclonal antibody Cy.002 light chain


Theoretical massNumber of molelcules
Total (without water)87,3993
Polymers87,3993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-29 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.050, 80.690, 117.360
Angle α, β, γ (deg.)90.000, 108.730, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cysteine-rich protective antigen / Inactive sialidase CyRPA / PfCyRPA


Mass: 40184.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: CyRPA, pfd1130w, PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#2: Antibody Monoclonal antibody Cy.002 heavy chain


Mass: 23525.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#3: Antibody Monoclonal antibody Cy.002 light chain


Mass: 23690.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M lithium sulfate, 30 % polyvinylpyrrolidone K15, 0.1 M HEPES pH7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→48.55 Å / Num. obs: 169805 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Net I/σ(I): 13.3
Reflection shellResolution: 2.72→2.81 Å / Num. unique obs: 15709 / CC1/2: 0.864

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-APR-2021)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIH

5tih


Resolution: 2.72→37.92 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.841 / SU R Cruickshank DPI: 2.35 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.453 / SU Rfree Blow DPI: 0.389 / SU Rfree Cruickshank DPI: 0.403
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 2096 4.28 %RANDOM
Rwork0.2728 ---
obs0.274 48960 99.8 %-
Displacement parametersBiso max: 229.92 Å2 / Biso mean: 100.55 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-21.2625 Å20 Å28.8946 Å2
2---38.2103 Å20 Å2
3---16.9478 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: final / Resolution: 2.72→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11867 0 0 76 11943
Biso mean---67.93 -
Num. residues----1377
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2054HARMONIC5
X-RAY DIFFRACTIONt_it12146HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1608SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8244SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d12146HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg16479HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion19.61
LS refinement shellResolution: 2.72→2.74 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3385 42 4.29 %
Rwork0.3862 938 -
all-980 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34970.3930.36240-0.27950.7409-0.06660.1144-0.04950.05440.02270.0494-0.03450.08590.0439-0.016-0.00670.0191-0.1167-0.0807-0.026319.7768-29.158141.8119
20.1776-0.3064-0.31430-0.46383.03440.1949-0.03490.0453-0.07910.13060.22120.02810.5628-0.3254-0.3040.0016-0.01230.304-0.16-0.23090.4216-29.786789.9358
30.6153-0.5402-1.30950.47081.08112.37240.0186-0.02740.12120.11480.1928-0.08050.190.1698-0.2114-0.01060.076-0.0006-0.001-0.1347-0.106-16.2608-23.725187.1643
41.98150.04930.88630.23040.21430.7780.0856-0.113-0.0497-0.1125-0.0552-0.07330.0301-0.1252-0.0305-0.03250.0197-0.0263-0.0982-0.0877-0.0262.747510.134741.0613
52.47040.2562-1.676801.92591.5955-0.1473-0.3650.50640.05850.41370.12330.23290.4509-0.2665-0.24750.1379-0.10370.304-0.1137-0.183239.195210.88684.5511
60.5406-0.4752-1.29510.01570.64742.9372-0.0111-0.07380.35720.16810.19850.04540.22970.5497-0.1874-0.16250.0939-0.07740.2169-0.1241-0.103330.37074.7591-9.7882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|361 }A31 - 361
2X-RAY DIFFRACTION2{ B|20 - B|238 }B20 - 238
3X-RAY DIFFRACTION3{ C|21 - C|236 }C21 - 236
4X-RAY DIFFRACTION4{ D|31 - D|362 }D31 - 362
5X-RAY DIFFRACTION5{ E|20 - E|238 }E20 - 238
6X-RAY DIFFRACTION6{ F|21 - F|236 }F21 - 236

+
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://pdbjlvh1.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