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- EMDB-22890: Plasmodium falciparum RhopH complex in soluble form -

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Basic information

Entry
Database: EMDB / ID: EMD-22890
TitlePlasmodium falciparum RhopH complex in soluble form
Map dataUnsharpened map
Sample
  • Complex: RhopH complex
    • Protein or peptide: Cytoadherence linked asexual protein 3
    • Protein or peptide: High molecular weight rhoptry protein-2
    • Protein or peptide: High molecular weight rhoptry protein 3
Function / homologyUncharacterized protein / High molecular weight rhoptry protein-2
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsSchureck MA / Darling JE / Merk A / Subramaniam S / Desai SA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Elife / Year: 2021
Title: Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake.
Authors: Marc A Schureck / Joseph E Darling / Alan Merk / Jinfeng Shao / Geervani Daggupati / Prakash Srinivasan / Paul Dominic B Olinares / Michael P Rout / Brian T Chait / Kurt Wollenberg / Sriram ...Authors: Marc A Schureck / Joseph E Darling / Alan Merk / Jinfeng Shao / Geervani Daggupati / Prakash Srinivasan / Paul Dominic B Olinares / Michael P Rout / Brian T Chait / Kurt Wollenberg / Sriram Subramaniam / Sanjay A Desai /
Abstract: Malaria parasites use the RhopH complex for erythrocyte invasion and channel-mediated nutrient uptake. As the member proteins are unique to Plasmodium spp., how they interact and traffic through ...Malaria parasites use the RhopH complex for erythrocyte invasion and channel-mediated nutrient uptake. As the member proteins are unique to Plasmodium spp., how they interact and traffic through subcellular sites to serve these essential functions is unknown. We show that RhopH is synthesized as a soluble complex of CLAG3, RhopH2, and RhopH3 with 1:1:1 stoichiometry. After transfer to a new host cell, the complex crosses a vacuolar membrane surrounding the intracellular parasite and becomes integral to the erythrocyte membrane through a PTEX translocon-dependent process. We present a 2.9 Å single-particle cryo-electron microscopy structure of the trafficking complex, revealing that CLAG3 interacts with the other subunits over large surface areas. This soluble complex is tightly assembled with extensive disulfide bonding and predicted transmembrane helices shielded. We propose a large protein complex stabilized for trafficking but poised for host membrane insertion through large-scale rearrangements, paralleling smaller two-state pore-forming proteins in other organisms.
History
DepositionOct 25, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7kiy
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22890.png

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Map

FileDownload / File: emd_22890.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.021953728 - 0.05335533
Average (Standard dev.)2.2393298e-05 (±0.001385021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0220.0530.000

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Supplemental data

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Additional map: Sharpened map

Fileemd_22890_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally sharpened map

Fileemd_22890_additional_2.map
AnnotationLocally sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_22890_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_22890_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RhopH complex

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

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Supramolecule #1: RhopH complex

SupramoleculeName: RhopH complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightExperimental: 434 KDa

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Macromolecule #1: Cytoadherence linked asexual protein 3

MacromoleculeName: Cytoadherence linked asexual protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 177.069516 KDa
SequenceString: MVSFFKTPII IFFFLLCLNE KVLCSINENE NLGENKNENA NVNTPENLNK LLNEYDNIEQ LKSMIGNDEL HKNLTILEKL ILESLEKDK LKYPLLKQGT EQLIDISKFN KKNITDADDE TYIIPTVQSS FHDIVKYEHL IKEQSIEIYN SDISDKIKKK I FIVRTLKT ...String:
MVSFFKTPII IFFFLLCLNE KVLCSINENE NLGENKNENA NVNTPENLNK LLNEYDNIEQ LKSMIGNDEL HKNLTILEKL ILESLEKDK LKYPLLKQGT EQLIDISKFN KKNITDADDE TYIIPTVQSS FHDIVKYEHL IKEQSIEIYN SDISDKIKKK I FIVRTLKT IKLMLIPLNS YKQNNDLKSA LEELNNVFTN KEAQKESSPI GDHGTFFRKL LTHVRTIKEN EDIENKGETL IL GDNKIDV MNSNDFFFTT NSNVKFMENL DDITNQYGLG LINHLGPHLI ALGHFTVLKL ALKNYKNYFE AKSIKFFSWQ KIL EFSMSD RFKVLDMMCD HESVYYSEKK RRKTYLKVDR SNTSMECNIL EYLLHYFNKY QLEIIKTTQD TDFDLHGMME HKYI KDYFF SFMCNDPKEC IIYHTNQFKK EANEENTFPE QEEPNRQISA FNLYLNYYYF MKRYSSYGVK KTLYVHLLNL TGLLN YDTR SYVTSLYLPG YYNAVEMSFT EEKEFSKLFE SLIQCIEKCH SDQARQISKD SNLLNDITKC DLCKGAFLYS NMKFDE VPS MLQKFYLYLT KGLKIQKVSS LIKTLDIYQD YSNFLSHDIN WYTFLFLFRL TSFKEISKKN VAEAMYLNIK DEDTFNK TI VTNYWYPSPI KKYYTLYVRK HIPNNLVDEL EKLMKSGTLE KMKKSLTFLV HVNSFLQLDF FHQLNEPPLG LPRSYPLS L VLEHKFKEWM DSSPAGFYFS NYQNPYVRKD LHDKVLSQKF EPPKMNQWNK VLKSLIECAY DMYFEQRHVK NLYKYHNIY NINNKLMLMR DSIDLYKTHF DDVLFFADIF NMRKYMTATP VYKKVKDRVY HTLHSITGNS VNFYKYGIIY GFKVNKEILK EVVDELYSI YNFNTDIFTD TSFLQTVYLL FRRIEETYRT QRRDDKISVN NVFFMNVANN YSKLNKEERE IEIHNSMASR Y YAKTMFAA FQMLFSTMLS NNVDNLDKAY GLSENIQVAT STSAFLTFAY VYNGSIMDSV TNSLLPPYAK KPITQLKYGK TF VFSNYFM LASKMYDMLN YKNLSLLCEY QAVASANFYS AKKVGQFIGR KFLPITTYFL VMRISWTHAF TTGQHLIAAF DPL NTNTSP KPNGGSGIYK SPESFFFTHA LAAEASKYLF FYFFTNLYLD AYKSFPGGFG PAIKEQTQHV QEQTYERKPS VHSF NRNFF MELANGFMYA FCFFAISQMY AYFENINFYI TSNFRFLDRY YGVFNKYFIN YARIKLKEIT SDLLIKYERE AYLSM KKYG YLGEVIAARL SPKDKIMNYV HETNDDVMSN LRRYDMENAF KNKMSTYVDD FAFFDDCGKN EQFLNERCDY CPVIEE VEE TELFTTTGDK NTNKTTEIKK QTSTYIDTEK MNEADSADSD DEKDSDTPDN ELMIARFHGA GHHHHHHHHH HDYKDDD DK GLVPRGSAAA AYPYDVPDYA SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK GPDRKAAVSH WQQ

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 162.877406 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 EDYYKLPLAP DMVKTYHCYK LGKQAAKLLE S IILKKKFV RFRVTDAIDV YDFFYIKKVL SSHIKKEYNE 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 104.981406 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 DELAGSEGPS 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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMTristris(hydroxymethyl)aminomethane
200.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K

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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) / Detector mode: COUNTING / Digitization - Frames/image: 1-58 / Number grids imaged: 1 / Number real images: 1310 / Average exposure time: 0.4 sec. / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 311390
Startup modelType of model: OTHER / Details: Initial model generated using RELION.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68216
DetailsAll cryo-EM image processing was performed in RELION 3.0.
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 97.81
Output model

PDB-7kiy:
Plasmodium falciparum RhopH complex in soluble form

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