[English] 日本語
Yorodumi
- PDB-5tih: Structural basis for inhibition of erythrocyte invasion by antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tih
TitleStructural basis for inhibition of erythrocyte invasion by antibodies to Plasmodium falciparum protein CyRPA
Components
  • CyRPA antibody Fab Heavy Chain
  • CyRPA antibody Fab Light Chain
  • Cysteine-rich protective antigen
KeywordsIMMUNE SYSTEM / Plasmodium falciparum CyRPA Inhibitory antibody
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 Å
AuthorsChen, L. / Xu, Y. / Wang, W. / Thompson, J.K. / Goddard-Borger, E. / Lawrence, M.C. / Cowman, A.F.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Elife / Year: 2017
Title: Structural basis for inhibition of erythrocyte invasion by antibodies toPlasmodium falciparumprotein CyRPA.
Authors: Chen, L. / Xu, Y. / Wong, W. / Thompson, J.K. / Healer, J. / Goddard-Borger, E.D. / Lawrence, M.C. / Cowman, A.F.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine-rich protective antigen
H: CyRPA antibody Fab Heavy Chain
L: CyRPA antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5396
Polymers86,3613
Non-polymers1773
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.950, 87.380, 145.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cysteine-rich protective antigen


Mass: 39485.402 Da / Num. of mol.: 1 / Fragment: UNP residues 30-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_0423800 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IFM8
#2: Antibody CyRPA antibody Fab Heavy Chain


Mass: 23343.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody CyRPA antibody Fab Light Chain


Mass: 23532.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 11% PEG5000 monomethyl ether 0.2M NaAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.44→38.339 Å / Num. obs: 38349 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.964 % / Biso Wilson estimate: 54.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.089 / Χ2: 0.983 / Net I/σ(I): 14.54 / Num. measured all: 228722 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.44-2.585.6190.9912.1732264586957420.7271.08897.8
2.58-2.766.2050.6293.5536547589358900.8660.68799.9
2.76-2.986.1960.3276.1733512541154090.9570.357100
2.98-3.266.1690.15911.0930618496849630.990.17399.9
3.26-3.656.0980.08518.4228270463946360.9960.09399.9
3.65-4.215.9950.05725.6523991401740020.9970.06299.6
4.21-5.145.810.04331.7219864343834190.9980.04899.4
5.14-7.235.5890.04431.3515186272627170.9980.04899.7
7.23-38.3395.3910.03534.58470162915710.9990.03896.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l9d

5l9d


Resolution: 2.44→38.339 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 1891 4.93 %
Rwork0.1887 36454 -
obs0.1898 38345 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.44 Å2 / Biso mean: 68.0314 Å2 / Biso min: 30.38 Å2
Refinement stepCycle: final / Resolution: 2.44→38.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 12 43 6045
Biso mean--68.68 51.99 -
Num. residues----750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036149
X-RAY DIFFRACTIONf_angle_d0.5768343
X-RAY DIFFRACTIONf_chiral_restr0.045914
X-RAY DIFFRACTIONf_plane_restr0.0031064
X-RAY DIFFRACTIONf_dihedral_angle_d13.0493675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4401-2.50110.2961200.28372495261596
2.5011-2.56870.32341310.294125742705100
2.5687-2.64430.38991340.285325812715100
2.6443-2.72960.27171450.255125452690100
2.7296-2.82720.25691290.254626042733100
2.8272-2.94030.27071310.24425812712100
2.9403-3.07410.2461390.234625942733100
3.0741-3.23610.30031220.236526222744100
3.2361-3.43870.2351260.2125972723100
3.4387-3.7040.2531500.200226052755100
3.704-4.07640.18661390.178426202759100
4.0764-4.66540.15581270.14272633276099
4.6654-5.87440.16111370.14626682805100
5.8744-38.34360.17261610.15352735289698
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)
12.0894-0.37920.05624.01322.67565.2269-0.22020.0644-0.01160.2018-0.03390.23810.2526-0.170.21810.4077-0.0616-0.03180.27560.06620.361972.282470.897193.0159
22.90620.10790.72513.9345-1.70855.5853-0.08220.2948-0.1685-0.28950.1897-0.43140.19940.4643-0.09530.3812-0.08880.02210.3203-0.05820.400789.322567.000893.4131
34.4771-2.2155-0.08232.21141.43292.5658-0.1628-0.55730.05180.43510.11780.23410.1518-0.0920.02480.49420.00170.03780.339-0.01160.416679.806471.6032111.4923
42.92651.27191.36295.33692.03276.93540.263-0.1607-0.64660.5834-0.0467-0.30770.69530.1931-0.24330.46930.0226-0.08250.30790.00290.52770.539347.798270.6755
50.356-0.3751-0.56151.46661.03197.5764-0.05460.3129-0.1398-0.02380.1096-0.02440.81470.7449-0.05050.44080.1071-0.070.5889-0.12340.590773.421947.427548.9513
65.09711.3139-4.11935.443-2.17576.80320.1174-0.4066-0.0895-0.1432-0.083-0.58530.63121.95130.02970.53780.1509-0.02171.1704-0.23360.500680.923145.283335.0116
75.8209-0.1465-1.97263.8240.4097.2081-0.04070.63340.1904-0.56040.11930.0613-1.2055-0.055-0.0860.5681-0.1195-0.07260.378-0.00340.374467.449971.044561.078
84.27982.7820.57936.2274-0.6735.6162-0.09340.35530.235-0.33040.1914-0.3789-0.6940.8476-0.11140.4392-0.11330.00760.4518-0.02860.35373.750368.904463.7737
92.07282.15791.20018.46484.68598.22150.16520.14190.0373-0.2385-0.05130.041-0.39220.7599-0.17420.4678-0.00240.07610.7302-0.1090.430471.103457.203231.8898
102.68621.95211.11952.9133.61957.6803-0.01680.3567-0.1191-1.3982-0.06790.4767-0.57320.01830.05990.70130.071-0.05330.8387-0.11340.542466.56953.23322.1192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 109 )A2 - 109
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 180 )A110 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 333 )A181 - 333
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 83 )H1 - 83
5X-RAY DIFFRACTION5chain 'H' and (resid 84 through 144 )H84 - 144
6X-RAY DIFFRACTION6chain 'H' and (resid 145 through 215 )H145 - 215
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 38 )L1 - 38
8X-RAY DIFFRACTION8chain 'L' and (resid 39 through 102 )L39 - 102
9X-RAY DIFFRACTION9chain 'L' and (resid 103 through 174 )L103 - 174
10X-RAY DIFFRACTION10chain 'L' and (resid 175 through 212 )L175 - 212

+
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