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- EMDB-23959: Native RhopH complex of the malaria parasite Plasmodium falciparum -

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Basic information

Entry
Database: EMDB / ID: EMD-23959
TitleNative RhopH complex of the malaria parasite Plasmodium falciparum
Map dataCryoEM density map of RhopH complex.
Sample
  • Complex: High molecular mass rhoptry protein complex (RhopH complex)
    • Protein or peptide: Cytoadherence linked asexual protein 3.1
    • Protein or peptide: High molecular weight rhoptry protein 2
    • Protein or peptide: High molecular weight rhoptry protein 3
Function / homologyCytoadherence-linked asexual protein / Cytoadherence-linked asexual protein / adhesion of symbiont to microvasculature / High molecular weight rhoptry protein 2 / Cytoadherence linked asexual protein 3.1 / High molecular weight rhoptry protein 3
Function and homology information
Biological speciesPlasmodium falciparum NF54 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsHo CM / Jih J / Lai M / Li XR / Goldberg DE / Beck JR / Zhou ZH
Funding support United States, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99/R00 HL133453 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007323 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition.
Authors: Chi-Min Ho / Jonathan Jih / Mason Lai / Xiaorun Li / Daniel E Goldberg / Josh R Beck / Z Hong Zhou /
Abstract: The RhopH complex is implicated in malaria parasites' ability to invade and create new permeability pathways in host erythrocytes, but its mechanisms remain poorly understood. Here, we enrich the ...The RhopH complex is implicated in malaria parasites' ability to invade and create new permeability pathways in host erythrocytes, but its mechanisms remain poorly understood. Here, we enrich the endogenous RhopH complex in a native soluble form, comprising RhopH2, CLAG3.1, and RhopH3, directly from parasite cell lysates and determine its atomic structure using cryo-electron microscopy (cryo-EM), mass spectrometry, and the cryoID program. CLAG3.1 is positioned between RhopH2 and RhopH3, which both share substantial binding interfaces with CLAG3.1 but make minimal contacts with each other. The forces stabilizing individual subunits include 13 intramolecular disulfide bonds. Notably, CLAG3.1 residues 1210 to 1223, previously predicted to constitute a transmembrane helix, are embedded within a helical bundle formed by residues 979 to 1289 near the C terminus of CLAG3.1. Buried in the core of the RhopH complex and largely shielded from solvent, insertion of this putative transmembrane helix into the erythrocyte membrane would likely require a large conformational rearrangement. Given the unusually high disulfide content of the complex, it is possible that such a rearrangement could be initiated by the breakage of allosteric disulfide bonds, potentially triggered by interactions at the erythrocyte membrane. This first direct observation of an exported transmembrane protein-in a soluble, trafficking state and with atomic details of buried putative membrane-insertion helices-offers insights into the assembly and trafficking of RhopH and other parasite-derived complexes to the erythrocyte membrane. Our study demonstrates the potential the endogenous structural proteomics approach holds for elucidating the molecular mechanisms of hard-to-isolate complexes in their native, functional forms.
History
DepositionMay 10, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mrw
  • Surface level: 0.0355
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23959.png

Downloads & links

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Map

FileDownload / File: emd_23959.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density map of RhopH complex.
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0355 / Movie #1: 0.0355
Minimum - Maximum-0.08641203 - 0.13304473
Average (Standard dev.)0.00039805658 (±0.004077589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ7371100
NX/NY/NZ11585169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0860.1330.000

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Supplemental data

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Sample components

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Entire : High molecular mass rhoptry protein complex (RhopH complex)

EntireName: High molecular mass rhoptry protein complex (RhopH complex)
Components
  • Complex: High molecular mass rhoptry protein complex (RhopH complex)
    • Protein or peptide: Cytoadherence linked asexual protein 3.1
    • Protein or peptide: High molecular weight rhoptry protein 2
    • Protein or peptide: High molecular weight rhoptry protein 3

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Supramolecule #1: High molecular mass rhoptry protein complex (RhopH complex)

SupramoleculeName: High molecular mass rhoptry protein complex (RhopH complex)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote) / Strain: NF54

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Macromolecule #1: Cytoadherence linked asexual protein 3.1

MacromoleculeName: Cytoadherence linked asexual protein 3.1 / type: protein_or_peptide / ID: 1
Details: CLAG3.1, subunit of the soluble form of the RhopH complex
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote) / Strain: isolate NF54
Molecular weightTheoretical: 167.444219 KDa
SequenceString: MVSFFKTPIF ILIIFLYLNE KVICSINENQ NENDTISQNV NQHENINQNV NDNDNIEQLK SMIGNDELHK NLTILEKLIL ESLEKDKLK YPLLKQGTEQ LIDISKFNKK NITDADDETY IIPTVQSTFH DIVKYEHLIK EQSIEIYNSD ISDKIKKKIF I VRTLKTIK ...String:
MVSFFKTPIF ILIIFLYLNE KVICSINENQ NENDTISQNV NQHENINQNV NDNDNIEQLK SMIGNDELHK NLTILEKLIL ESLEKDKLK YPLLKQGTEQ LIDISKFNKK NITDADDETY IIPTVQSTFH DIVKYEHLIK EQSIEIYNSD ISDKIKKKIF I VRTLKTIK LMLIPLNSYK QNNDLKSALE ELNNVFTNKE AQEESSPIGD HGTFFRKLLT HVRTIKENED IENKGETLIL GD NKIDVMN SNDFFFTTNS NVKFMENLDD ITNQYGLGLI NHLGPHLIAL GHFTVLKLAL KNYKNYFEAK SIKFFSWQKI LEF SMSDRF KVLDMMCDHE SVYYSEKKRR KTYLKVDRSN TSMECNILEY LLHYFNKYQL EIIKTTQDTD FDLHGMMEHK YIKD YFFSF MCNDPKECII YHTNQFKKEA NEENTFPEQE EPNRQISAFN LYLNYYYFMK RYSSYGVKKT LYVHLLNLTG LLNYD TRAY VTSLYLPGYY NAVEMSFTEE KEFSKLFESL IQCIEKCHSD QARQISKDSN LLNNITKCDL CKGAFLYANM KFDEVP SML QKFYVYLTKG LKIQKVSSLI KTLDIYQDYS NYLSHDINWY TFLFLFRLTS FKEIAKKNVA EAMYLNIKDE DTFNKTV VT NYWYPSPIKK YYTLYVRKHI PNNLVDELEK LMKSGTLEKM KKSLTFLVHV NSFLQLDFFH QLNEPPLGLP RSYPLSLV L EHKFKEWMNS SPAGFYFSNY QNPYIRKDLH DKVLSQKFEP PKMNQWNKVL KSLIECAYDM YFEQRHVKNL YKYHNIYNI NNKLMLMRDS IDLYKNNFDD VLFFADIFNM RKYMTATPVY KKVKDRVYHT LHSITGNSVN FYKYGIIYGF KVNKEILKEV VDELYSIYN FNTDIFTDTS FLQTVYLLFR RIEETYRTQR RDDKISVNNV FFMNVANNYS KLNKEEREIE IHNSMASRYY A KTMFAAFQ MLFSTMLSNN VDNLDKAYGL SENIQVATST SAFLTFAYVY NGSIMDSVTN SLLPPYAKKP ITQLKYGKTF VF SNYFMLA SKMYDMLNYK NLSLLCEYQA VASANFYSAK KVGQFLGRKF LPITTYFLVM RISWTHAFTT GQHLISAFGS PSS TANGKS NASGYKSPES FFFTHGLAAE ASKYLFFYFF TNLYLDAYKS FPGGFGPAIK EQTQHVQEQT YERKPSVHSF NRNF FMELV NGFMYAFCFF AISQMYAYFE NINFYITSNF RFLDRYYGVF NKYFINYAII KLKEITSDLL IKYEREAYLS MKKYG YLGE VIAARLSPKD KIMNYVHETN EDIMSNLRRY DMENAFKNKM STYVDDFAFF DDCGKNEQFL NERCDYCPVI EEVEET QLF TTTGDKNTNK TTEIKKQTST YIDTEKMNEA DSADSDDEKD SDTPDDELMI SRFH

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Macromolecule #2: High molecular weight rhoptry protein 2

MacromoleculeName: High molecular weight rhoptry protein 2 / type: protein_or_peptide / ID: 2
Details: RhopH2, subunit of the soluble form of the RhopH complex
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote) / Strain: isolate NF54
Molecular weightTheoretical: 162.886344 KDa
SequenceString: MIKVTIFLLL SIFSFNLYGL ELNEKVSIKY GAEQGVGSAD SNTKLCSDIL KYLYMDEYLS EGDKATFEKK CHNVIGNIRN TFSNKNTIK EGNEFLMSIL HMKSLYGNNN NNNAGSESDV TLKSLYLSLK GSQNTEGESE VPSDDEINKT IMNFVKFNKY L LDNSNDIK ...String:
MIKVTIFLLL SIFSFNLYGL ELNEKVSIKY GAEQGVGSAD SNTKLCSDIL KYLYMDEYLS EGDKATFEKK CHNVIGNIRN TFSNKNTIK EGNEFLMSIL HMKSLYGNNN NNNAGSESDV TLKSLYLSLK GSQNTEGESE VPSDDEINKT IMNFVKFNKY L LDNSNDIK KVHDFLVLTS QSNENLLPNK EKLFEQIVDQ IKYFDEYFFA SGGKIKVKKG YLKYNFLDIY KQPVCSAYLH LC SRYYESV SIYIRLKKVF NGIPAFLDKN CRKVKGEEFK KLMDMELKHN HIVERFDKYI ISDDLYYVNM KVFDLKNVDK IQV SKIDDI NNLNIYEHKE TMHLSAKNLS RYIDIKKELN DEKAYKQLMS AIRKYVTTLT KADSDITYFV KQLDDEEIER FLID LNFFL YNGFLRITED KHLINADDVS PSYINLYRSN NIVALYILKT QYEENKLSEY RAHKFYRRKR VSNITNDMIK KDFTQ TNAL TNLPNLDNKK TTEYYLKEYE NFVENFQPDL HDIMKLQLFF TMAFKDCNVN QNFTETSKKL WFDLLYAYDK FGWFYI HPN EVINSINKTD FVRHVLVSRN FLLKNNDQLT FLETQVAKIV EIINLSLEVD KSPDSLDFSI PMNFFNHKNG YHVMNDD KL KLLTSYEYID SIANNYFFLS EYKNDVFRTG NNFKLYFNLP NIYSLAYQLF NELAININVI TNVPLKKYLK YNASYAYF T LMNMIGKNHD IYSKGSRFVY ASYILGLVFF IESHIDIARL KPKDFFFMKQ SLPIIDHVYH KDLKTLKKNC TLLTDFMKI NKNSQNYSLT HTEEMIKILG LLTVTLWAKE GKKSVYYDDD VSLYRKLMVS CVFNGGETIQ EKLANNIEKS CDISQYGIKS KNLKDMIDI NLSIHKWNPA EIEKLAYSFV LSCKMQKLMY KPMNVEKLPL EDYYKLSLAP DMVKTYHCYK LGKQAAELLE S IILKKKFV RFRVTDAIDV YDFFYIKKVL SSRIKKEYNE FLQDKRAFEK KELETILNNS PFSEEQTMKL INSYECHWFT SY ENFRILW MHASSNLGTG TYLKNFFSEL WQNIRFLFKS KLKIRDMEYF SGDISQMNLL DYYSPMVHSE SHCQEKMQVL FIT LRDSKE ENRSEIAQKV KSAYYQCKLD YYKNHHSDFI HRIHPNDFLN NKVYVLKQPY YLMSNVPLNN PKKVSRLFVT EGTL EYLLL DKINIPECFG PCTKLHFNKV VIKESKQRIY DMTINNALVP EIQPYNRRKY MTIYINEAYI KNIVSDALTS EEIKR HDIQ KGNIKICMGK STYLTEPILT EEHFNLTHKP VYDFSSVKHN LKVFHMKNEH LVSEDPNDDC FINYPLATIN LDISDP YKE ISEDLIKNLY ILKSS

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Macromolecule #3: High molecular weight rhoptry protein 3

MacromoleculeName: High molecular weight rhoptry protein 3 / type: protein_or_peptide / ID: 3
Details: RhopH3, subunit of the soluble form of the RhopH complex
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote) / Strain: isolate NF54
Molecular weightTheoretical: 104.997406 KDa
SequenceString: MRSKHLVTLF IITFLSFSTV KVWGKDVFAG FVTKKLKTLL DCNFALYYNF KGNGPDAGSF LDFVDEPEQF YWFVEHFLSV KFRVPKHLK DKNIHNFTPC LNRSWVSEFL KEYEEPFVNP VMKFLDKEQR LFFTYNFGDV EPQGKYTYFP VKEFHKYCIL P PLIKTNIK ...String:
MRSKHLVTLF IITFLSFSTV KVWGKDVFAG FVTKKLKTLL DCNFALYYNF KGNGPDAGSF LDFVDEPEQF YWFVEHFLSV KFRVPKHLK DKNIHNFTPC LNRSWVSEFL KEYEEPFVNP VMKFLDKEQR LFFTYNFGDV EPQGKYTYFP VKEFHKYCIL P PLIKTNIK DGESGEFLKY QLNKEEYKVF LSSVGSQMTA IKNLYSTVED EQRKQLLKVI IENESTNDIS VQCPTYNIKL HY TKECANS NNILKCIDEF LRKTCEKKTE SKHPSADLCE HLQFLFESLK NPYLDNFKKF MTNSDFTLIK PQSVWNVPIF DIY KPKNYL DSVQNLDTEC FKKLNSKNLI FLSFHDDIPN NPYYNVELQE IVKLSTYTYS IFDKLYNFFF VFKKSGAPIS PVSV KELSH NITDFSFKED NSEIQCQNVR KSLDLEVDVE TMKGIAAEKL CKIIEKFILT KDDASKPEKS DIHRGFRILC ILIST HVEA YNIVRQLLNM ESMISLTRYT SLYIHKFFKS VTLLKGNFLY KNNKAIRYSR ACSKASLHVP SVLYRRNIYI PETFLS LYL GLSNLVSSNP SSPFFEYAII EFLVTYYNKG SEKFVLYFIS IISVLYINEY YYEQLSCFYP KEFELIKSRM IHPNIVD RI LKGIDNLMKS TRYDKMRTMY LDFESSDIFS REKVFTALYN FDSFIKTNEQ LKKKNLEEIS EIPVQLETSN DGIGYRKQ D VLYETDKPQT MDEASYEETV DEDAHHVNEK QHSAHFLDAI AEKDILEEKT KDQDLEIELY KYMGPLKEQS KSTSAASTS DEISGSEGPS TESTSTGNQG EDKTTDNTYK EMEELEEAEG TSNLKKGLEF YKSSLKLDQL DKEKPKKKKS KRKKKRDSSS DRILLEESK TFTSENEL

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2900167
CTF correctionSoftware - Name: cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 108872

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7mrw:
Native RhopH complex of the malaria parasite Plasmodium falciparum

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