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- EMDB-7784: Cryo-EM structure of a Plasmodium vivax invasion complex essentia... -

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Entry
Database: EMDB / ID: EMD-7784
TitleCryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 1.
Map dataCryo-EM structure of the ternary complex between human transferrin receptor 1, transferrin and Plasmodium vivax reticulocyte-binding protein 2b; two molecules of parasite ligand, subclass 1.
Sample
  • Complex: ternary complex between human transferrin receptor 1, transferrin and Plasmodium vivax reticulocyte-binding protein 2b
    • Protein or peptide: Transferrin receptor protein 1
    • Protein or peptide: Serotransferrin
    • Protein or peptide: Reticulocyte binding protein 2, putative
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FE (III) ION
  • Ligand: CARBONATE ION
Keywordsmalaria / Plasmodium vivax / reticulocyte / invasion / CELL INVASION
Function / homology
Function and homology information


transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of cell motility / response to iron ion / response to copper ion / RND1 GTPase cycle / RND2 GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / endocytic vesicle / RHOH GTPase cycle / RHOG GTPase cycle / transport across blood-brain barrier / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / positive regulation of T cell proliferation / positive regulation of phosphorylation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / ERK1 and ERK2 cascade / osteoclast differentiation / ferric iron binding / response to nutrient / basal plasma membrane / cellular response to leukemia inhibitory factor / actin filament organization / acute-phase response / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of iron ion transport / regulation of protein stability / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / recycling endosome membrane / double-stranded RNA binding / late endosome / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / antibacterial humoral response / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / apical plasma membrane / endoplasmic reticulum lumen / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / cell surface
Similarity search - Function
NBD94 domain / Nucleotide-Binding Domain 94 of RH / Transferrin receptor protein 1/2, PA domain / Serotransferrin, mammalian / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain ...NBD94 domain / Nucleotide-Binding Domain 94 of RH / Transferrin receptor protein 1/2, PA domain / Serotransferrin, mammalian / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Reticulocyte binding protein 2, putative / Transferrin receptor protein 1 / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human) / Plasmodium vivax (malaria parasite P. vivax)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsGruszczyk J / Huang RK
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of an essential Plasmodium vivax invasion complex.
Authors: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / ...Authors: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / Zhiheng Yu / Wai-Hong Tham /
Abstract: Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. ...Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 Å resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.
History
DepositionApr 10, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseJun 20, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6d04
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7784.png

Downloads & links

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Map

FileDownload / File: emd_7784.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the ternary complex between human transferrin receptor 1, transferrin and Plasmodium vivax reticulocyte-binding protein 2b; two molecules of parasite ligand, subclass 1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 180 pix.
= 243. Å		1.35 Å/pix.
x 180 pix.
= 243. Å		1.35 Å/pix.
x 180 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075 / Movie #1: 0.075
Minimum - Maximum-0.27329788 - 0.3753413
Average (Standard dev.)0.0022140185 (±0.015423093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z243.000243.000243.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.2730.3750.002

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Supplemental data

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Sample components

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Entire : ternary complex between human transferrin receptor 1, transferrin...

EntireName: ternary complex between human transferrin receptor 1, transferrin and Plasmodium vivax reticulocyte-binding protein 2b
Components
  • Complex: ternary complex between human transferrin receptor 1, transferrin and Plasmodium vivax reticulocyte-binding protein 2b
    • Protein or peptide: Transferrin receptor protein 1
    • Protein or peptide: Serotransferrin
    • Protein or peptide: Reticulocyte binding protein 2, putative
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FE (III) ION
  • Ligand: CARBONATE ION

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Supramolecule #1: ternary complex between human transferrin receptor 1, transferrin...

SupramoleculeName: ternary complex between human transferrin receptor 1, transferrin and Plasmodium vivax reticulocyte-binding protein 2b
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: two molecules of parasite ligand, subclass 1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transferrin receptor protein 1

MacromoleculeName: Transferrin receptor protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.940477 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ADPHHHHHHS SGIEGRGEFR LYWDDLKRKL SEKLDSTDFT STIKLLNENS YVPREAGSQK DENLALYVEN QFREFKLSKV WRDQHFVKI QVKDSAQNSV IIVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG K ITFAEKVA ...String:
ADPHHHHHHS SGIEGRGEFR LYWDDLKRKL SEKLDSTDFT STIKLLNENS YVPREAGSQK DENLALYVEN QFREFKLSKV WRDQHFVKI QVKDSAQNSV IIVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG K ITFAEKVA NAESLNAIGV LIYMDQTKFP IVNAELSFFG HAHLGTGDPY TPGFPSFNHT QFPPSRSSGL PNIPVQTISR AA AEKLFGN MEGDCPSDWK TDSTCRMVTS ESKNVKLTVS NVLKEIKILN IFGVIKGFVE PDHYVVVGAQ RDAWGPGAAK SGV GTALLL KLAQMFSDMV LKDGFQPSRS IIFASWSAGD FGSVGATEWL EGYLSSLHLK AFTYINLDKA VLGTSNFKVS ASPL LYTLI EKTMQNVKHP VTGQFLYQDS NWASKVEKLT LDNAAFPFLA YSGIPAVSFC FCEDTDYPYL GTTMDTYKEL IERIP ELNK VARAAAEVAG QFVIKLTHDV ELNLDYERYN SQLLSFVRDL NQYRADIKEM GLSLQWLYSA RGDFFRATSR LTTDFG NAE KTDRFVMKKL NDRVMRVEYH FLSPYVSPKE SPFRHVFWGS GSHTLPALLE NLKLRKQNNG AFNETLFRNQ LALATWT IQ GAANALSGDV WDIDNEF

UniProtKB: Transferrin receptor protein 1

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Macromolecule #2: Serotransferrin

MacromoleculeName: Serotransferrin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.153906 KDa
SequenceString: MRLAVGALLV CAVLGLCLAV PDKTVRWCAV SEHEATKCQS FRDHMKSVIP SDGPSVACVK KASYLDCIRA IAANEADAVT LDAGLVYDA YLAPNNLKPV VAEFYGSKED PQTFYYAVAV VKKDSGFQMN QLRGKKSCHT GLGRSAGWNI PIGLLYCDLP E PRKPLEKA ...String:
MRLAVGALLV CAVLGLCLAV PDKTVRWCAV SEHEATKCQS FRDHMKSVIP SDGPSVACVK KASYLDCIRA IAANEADAVT LDAGLVYDA YLAPNNLKPV VAEFYGSKED PQTFYYAVAV VKKDSGFQMN QLRGKKSCHT GLGRSAGWNI PIGLLYCDLP E PRKPLEKA VANFFSGSCA PCADGTDFPQ LCQLCPGCGC STLNQYFGYS GAFKCLKDGA GDVAFVKHST IFENLANKAD RD QYELLCL DNTRKPVDEY KDCHLAQVPS HTVVARSMGG KEDLIWELLN QAQEHFGKDK SKEFQLFSSP HGKDLLFKDS AHG FLKVPP RMDAKMYLGY EYVTAIRNLR EGTCPEAPTD ECKPVKWCAL SHHERLKCDE WSVNSVGKIE CVSAETTEDC IAKI MNGEA DAMSLDGGFV YIAGKCGLVP VLAENYNKSD NCEDTPEAGY FAVAVVKKSA SDLTWDNLKG KKSCHTAVGR TAGWN IPMG LLYNKINHCR FDEFFSEGCA PGSKKDSSLC KLCMGSGLNL CEPNNKEGYY GYTGAFRCLV EKGDVAFVKH QTVPQN TGG KNPDPWAKNL NEKDYELLCL DGTRKPVEEY ANCHLARAPN HAVVTRKDKE ACVHKILRQQ QHLFGSNVTD CSGNFCL FR SETKDLLFRD DTVCLAKLHD RNTYEKYLGE EYVKAVGNLR KCSTSSLLEA CTFRRP

UniProtKB: Serotransferrin

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Macromolecule #3: Reticulocyte binding protein 2, putative

MacromoleculeName: Reticulocyte binding protein 2, putative / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax) / Strain: Salvador I
Molecular weightTheoretical: 96.798477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSMHIPI QPSPESTQST NTTDNIDYFD ISDESNYYLI SQLRPHFSNI YFFDEFKRYA SYHTEIKRYE DIHKTKVNSL LNEASRAIG ICNRAKNTVK GLINILENPQ KFKTQRESYD VKLRQYEEKK EAFRGCLLNK NRKNLDQIKK INNEIRDLLE K LKCSQDCQ ...String:
GAMGSMHIPI QPSPESTQST NTTDNIDYFD ISDESNYYLI SQLRPHFSNI YFFDEFKRYA SYHTEIKRYE DIHKTKVNSL LNEASRAIG ICNRAKNTVK GLINILENPQ KFKTQRESYD VKLRQYEEKK EAFRGCLLNK NRKNLDQIKK INNEIRDLLE K LKCSQDCQ TNVYFDMIKI YLVDFKKMPY ENYDTFIKQY KNSYLSGVDM IRKIEKQIDN PVTINAIKFT QKEMGYIIDR FE YHLQKVK HSIDQVTALS DGVKPKQVTK NRLKEYYFNI GNYYSIFKFG KDSLNMLNKA LIHKEKIVHN LLGELFGHLE ERI SKLIDS EYFITESNNI ISQSEETLKL AEDVYDKNTK LIEDLTLYPH LEINEFKKDY DNNVEDLRES IIYIQSYVSS IKSA YRYNV LEKDSVESKQ KNIPANSNAQ KKVDELLSII DSISYSNFSV AENFQKMKDY YKEIEKLKIK ILQLIEAIKK YQQHV EELI NKEKAVAILK EDINKIIEYI KGIIEKLKQL ISANKDFDKI FQQVEQLINE ALFNKDQFEH NKNDLHTKMK EIMHTF HER DLQQFLDNMS KFLKDQEASY QNADSKEKLD QLLTTVKAKQ DELKEMKCDD IPDIIDNLKK ESQNVLNLKD EVINKQF EN MRTEMSSSLD QMTKEYNALK SSIEEYEAEK KGIENHKQNI IKRKNTFIVA EHENDEDVPE GKNTYNEFIS NKDTILQK E SAISNQMNTL EEKKRNRKTT LQTYGDAIQK LETYTEKKDE ETKVLLDKFN TEVENFKLDE DEKSFNDAKS IVSNTINEV ENENKNIDSI KKVNIAMKRS

UniProtKB: Reticulocyte binding protein 2, putative

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #8: CARBONATE ION

MacromoleculeName: CARBONATE ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: CO3
Molecular weightTheoretical: 60.009 Da
Chemical component information

ChemComp-CO3:
CARBONATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormula
20.0 mMNaHEPES
100.0 mMNaCl
50.0 mMNaHC)3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average exposure time: 15.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1suv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287253
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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