[English] 日本語
Yorodumi
- PDB-6wno: Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wno
TitlePlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 243244
Components
  • 243244 Fab heavy chain
  • 243244 Fab light chain
  • Plasmodium vivax reticulocyte binding protein 2b
KeywordsCELL INVASION / invasion / plasmodium vivax / malaria / antibody complex
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Reticulocyte binding protein 2, putative
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsChan, L.J. / Dietrich, M.H. / Tham, W.H.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1160042 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1143187 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1154937 Australia
Wellcome Trust208693/Z/17/Z Australia
CitationJournal: Nat Commun / Year: 2021
Title: Naturally acquired blocking human monoclonal antibodies to Plasmodium vivax reticulocyte binding protein 2b.
Authors: Chan, L.J. / Gandhirajan, A. / Carias, L.L. / Dietrich, M.H. / Vadas, O. / Visentin, R. / Franca, C.T. / Menant, S. / Soldati-Favre, D. / Mueller, I. / King, C.L. / Tham, W.H.
History
DepositionApr 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 243244 Fab heavy chain
C: 243244 Fab light chain
A: Plasmodium vivax reticulocyte binding protein 2b
D: Plasmodium vivax reticulocyte binding protein 2b
E: 243244 Fab heavy chain
F: 243244 Fab light chain


Theoretical massNumber of molelcules
Total (without water)170,0136
Polymers170,0136
Non-polymers00
Water00
1
B: 243244 Fab heavy chain
C: 243244 Fab light chain
A: Plasmodium vivax reticulocyte binding protein 2b


Theoretical massNumber of molelcules
Total (without water)85,0073
Polymers85,0073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Plasmodium vivax reticulocyte binding protein 2b
E: 243244 Fab heavy chain
F: 243244 Fab light chain


Theoretical massNumber of molelcules
Total (without water)85,0073
Polymers85,0073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.010, 84.440, 90.910
Angle α, β, γ (deg.)90.730, 110.120, 103.090
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody 243244 Fab heavy chain


Mass: 24957.855 Da / Num. of mol.: 2 / Fragment: human antibody Fab heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody 243244 Fab light chain


Mass: 23528.900 Da / Num. of mol.: 2 / Fragment: human antibody Fab light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein Plasmodium vivax reticulocyte binding protein 2b


Mass: 36519.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_094255 / Plasmid: pET32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A5K736
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris chloride pH 8.5, 20% (w/v) PEG monomethyl ether 2,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.35→42.996 Å / Num. obs: 23223 / % possible obs: 97.7 % / Redundancy: 3.499 % / Biso Wilson estimate: 62.313 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.216 / Χ2: 0.846 / Net I/σ(I): 6.9 / Num. measured all: 81267 / Scaling rejects: 33
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
3.35-3.443.470.8381.595808171916740.6850.98897.4
3.44-3.533.6470.7131.986262176017170.7110.83697.6
3.53-3.633.6340.5942.45927166016310.7660.69898.3
3.63-3.753.610.5182.815617159115560.8470.6197.8
3.75-3.873.5590.4753.195530159815540.8370.56297.2
3.87-43.4970.4144.045141152314700.8630.49296.5
4-4.163.5090.2925.185056146414410.920.34698.4
4.16-4.323.4210.1976.724714140613780.9620.23498
4.32-4.523.1950.1737.424150133112990.9630.20997.6
4.52-4.743.3280.1498.64243130712750.9710.17997.6
4.74-4.993.3430.1438.734025123812040.9730.1797.3
4.99-5.33.6110.1439.124099114911350.9780.16898.8
5.3-5.663.6540.1528.63979110510890.9750.17998.6
5.66-6.123.6010.1478.353601101910000.9780.17398.1
6.12-6.73.6150.1299.1232799189070.9850.15298.8
6.7-7.493.5290.10411.3529718558420.9880.12298.5
7.49-8.653.2230.06415.4222987457130.9940.07895.7
8.65-10.593.2930.04121.1119766326000.9970.04994.9
10.59-14.983.5680.04223.6417414924880.9980.0599.2
14.98-42.9963.40.04424.668502652500.9970.05294.3

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W53

5w53


Resolution: 3.35→42.996 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 31.07
RfactorNum. reflection% reflection
Rfree0.2835 1158 4.99 %
Rwork0.2446 --
obs0.2466 23187 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.73 Å2 / Biso mean: 75.0202 Å2 / Biso min: 34.47 Å2
Refinement stepCycle: final / Resolution: 3.35→42.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10596 0 0 0 10596
Num. residues----1442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.35-3.50240.34551450.3018273698
3.5024-3.6870.36721440.285275598
3.687-3.91780.28651440.269274197
3.9178-4.22010.2861440.2481275398
4.2201-4.64430.2891460.2228277798
4.6443-5.31530.24211460.2239276498
5.3153-6.69270.30321460.2649277399

+
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