[English] 日本語
Yorodumi
- PDB-7unb: Crystal structure of malaria transmission-blocking antigen Pfs48/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7unb
TitleCrystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex with human antibodies RUPA-117 and RUPA-47
Components
  • (RUPA-117 Fab ...) x 2
  • Gametocyte surface protein P45/48
  • RUPA-47 Fab heavy chain
  • RUPA-47 Fab kappa chain
KeywordsIMMUNE SYSTEM / Pfs48/45 / human transmission-blocking antibodies / Plasmodium falciparum / Malaria
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsHailemariam, S. / McLeod, B. / Julien, J.-P.
Funding support United States, Canada, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148557-01A1 United States
Bill & Melinda Gates FoundationOPP1156262 United States
Canadian Institutes of Health Research (CIHR)428410 Canada
Bill & Melinda Gates FoundationOPP1179906 United States
CIFAR Azrieli Global Scholars Canada
Ontario Early Researcher Awards Canada
Canada Research Chairs Canada
CitationJournal: Immunity / Year: 2022
Title: Vaccination with a structure-based stabilized version of malarial antigen Pfs48/45 elicits ultra-potent transmission-blocking antibody responses.
Authors: McLeod, B. / Mabrouk, M.T. / Miura, K. / Ravichandran, R. / Kephart, S. / Hailemariam, S. / Pham, T.P. / Semesi, A. / Kucharska, I. / Kundu, P. / Huang, W.C. / Johnson, M. / Blackstone, A. / ...Authors: McLeod, B. / Mabrouk, M.T. / Miura, K. / Ravichandran, R. / Kephart, S. / Hailemariam, S. / Pham, T.P. / Semesi, A. / Kucharska, I. / Kundu, P. / Huang, W.C. / Johnson, M. / Blackstone, A. / Pettie, D. / Murphy, M. / Kraft, J.C. / Leaf, E.M. / Jiao, Y. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Ramjith, J. / King, C.R. / MacGill, R.S. / Wu, Y. / Lee, K.K. / Jore, M.M. / King, N.P. / Lovell, J.F. / Julien, J.P.
History
DepositionApr 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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
L: RUPA-47 Fab kappa chain
R: Gametocyte surface protein P45/48
E: RUPA-117 Fab kappa chain
H: RUPA-47 Fab heavy chain
F: RUPA-117 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7296
Polymers111,5085
Non-polymers2211
Water10,701594
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)73.669, 127.160, 132.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 4 types, 4 molecules LEHF

#1: Antibody RUPA-47 Fab kappa chain


Mass: 23490.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293F / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#3: Antibody RUPA-117 Fab kappa chain


Mass: 23523.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293S / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#4: Antibody RUPA-47 Fab heavy chain


Mass: 23725.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293F / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#5: Antibody RUPA-117 Fab heavy chain


Mass: 24253.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293S / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney

-
Protein / Sugars / Non-polymers , 3 types, 596 molecules R

#2: Protein Gametocyte surface protein P45/48


Mass: 16515.447 Da / Num. of mol.: 1 / Mutation: G397L, H308Y, and I402V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700 / Cell (production host): epithelial / Cell line (production host): 293S / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney / References: UniProt: Q8I6T1
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 25 % (w/v) polyethylene glycol 3350, and 0.1 M Tris

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.18→29.43 Å / Num. obs: 65804 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.059 / Net I/σ(I): 8.7
Reflection shellResolution: 2.18→2.21 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2596 / CC1/2: 0.603 / Rpim(I) all: 0.281 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXv1.17.1-3660refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GHG for RUPA-47; unpublished in-house structure for other components

6ghg


Resolution: 2.18→29.43 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 2006 3.05 %
Rwork0.178 63715 -
obs0.1798 65721 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.08 Å2 / Biso mean: 33.1884 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: final / Resolution: 2.18→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 14 594 8338
Biso mean--63.25 36.42 -
Num. residues----1017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.18-2.230.3411420.265445134655
2.23-2.290.28521420.249344874629
2.29-2.360.2891340.229544784612
2.36-2.440.31351510.2244884639
2.44-2.530.25661370.211345184655
2.53-2.630.28481430.210745154658
2.63-2.750.26871440.207244934637
2.75-2.890.25851410.204645264667
2.89-3.070.23031450.18745494694
3.07-3.310.20721350.175345484683
3.31-3.640.22591440.164645564700
3.64-4.170.21421500.149945944744
4.17-5.240.16761460.126946494795
5.25-29.430.19071520.168948014953
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)
10.9781.0945-0.19552.8748-0.07730.18820.03080.08530.22140.1490.04440.0865-0.09210.032-0.07230.22290.00530.00870.28190.00750.2536-7.35827.31519.712
20.29520.263-0.27730.4189-0.26950.5236-0.05660.04350.0301-0.05810.052-0.02230.0651-0.00450.01260.20640.0089-0.00960.2306-0.00710.22065.7133.193-36.189
30.62570.387-0.11562.11620.45070.80790.0407-0.14140.11260.04850.0131-0.1356-0.13150.0892-0.06080.1875-0.00110.01020.2933-0.02360.256410.48725.78418.684
41.64680.1187-0.65512.3335-0.13072.5983-0.0245-0.0456-0.08120.12570.00470.03990.13050.06470.02630.1752-0.0182-0.0260.1856-0.01740.166-5.286-14.8154.174
50.64930.4136-0.79670.7998-0.89971.96110.08330.02780.16930.09260.01670.1767-0.2004-0.0027-0.12610.2288-0.00070.00740.2352-0.00220.30725.49720.714-31.267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:214 )H1 - 214
2X-RAY DIFFRACTION2( CHAIN F AND ( RESID 1:216 OR RESID 301:301 ) )F1 - 216
3X-RAY DIFFRACTION2( CHAIN F AND ( RESID 1:216 OR RESID 301:301 ) )F301
4X-RAY DIFFRACTION3( CHAIN L AND RESID 1:213 )L1 - 213
5X-RAY DIFFRACTION4( CHAIN R AND RESID 292:429 )R292 - 429
6X-RAY DIFFRACTION5( CHAIN E AND RESID 1:214 )E1 - 214

+
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