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- EMDB-11150: Merozoite surface protein 1 (MSP-1) from Plasmodium falciparum, m... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11150 | |||||||||
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Title | Merozoite surface protein 1 (MSP-1) from Plasmodium falciparum, main conformation | |||||||||
![]() | Unfiltered map | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Dijkman PM / Kudryashev M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the merozoite surface protein 1 from . Authors: Patricia M Dijkman / Tanja Marzluf / Yingyi Zhang / Shih-Ying Scott Chang / Dominic Helm / Michael Lanzer / Hermann Bujard / Mikhail Kudryashev / ![]() Abstract: The merozoite surface protein 1 (MSP-1) is the most abundant protein on the surface of the erythrocyte-invading merozoite, the causative agent of malaria. MSP-1 is essential for merozoite formation, ...The merozoite surface protein 1 (MSP-1) is the most abundant protein on the surface of the erythrocyte-invading merozoite, the causative agent of malaria. MSP-1 is essential for merozoite formation, entry into and escape from erythrocytes, and is a promising vaccine candidate. Here, we present monomeric and dimeric structures of full-length MSP-1. MSP-1 adopts an unusual fold with a large central cavity. Its fold includes several coiled-coils and shows structural homology to proteins associated with membrane and cytoskeleton interactions. MSP-1 formed dimers through these domains in a concentration-dependent manner. Dimerization is affected by the presence of the erythrocyte cytoskeleton protein spectrin, which may compete for the dimerization interface. Our work provides structural insights into the possible mode of interaction of MSP-1 with erythrocytes and establishes a framework for future investigations into the role of MSP-1 in infection and immunity. #1: ![]() Title: Structure of the merozoite surface protein 1 from Plasmodium falciparum Authors: Dijkman PM / Marzluf T / Zhang Y / Chang SYS / Helm D / Lanzer M / Bujard H / Kudryashev M | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 45.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 36.8 KB 36.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.9 KB | Display | ![]() |
Images | ![]() | 121.8 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 86 MB 44.1 MB 35.9 MB 35.1 MB 82.4 MB 81.2 MB 49.6 MB 84.5 MB 84.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zbcMC ![]() 6zbdC ![]() 6zbeC ![]() 6zbfC ![]() 6zbgC ![]() 6zbhC ![]() 6zbjC ![]() 6zblC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 34.0 TB Data #1: Unaligned movies of MSP-1 [micrographs - multiframe] Data #2: Unaligned movies of hdMSP-1 (dataset 1) [micrographs - multiframe] Data #3: Unaligned movies of hdMSP-1 (dataset 2) [micrographs - multiframe] Data #4: Unaligned movies of hdMSP-1 (dataset 3) [micrographs - multiframe] Data #5: Unaligned movies of hdMSP-1 (dataset 4) [micrographs - multiframe] Data #6: Final particle stack for hdMSP-1 conformation 1 [picked particles - single frame - processed] Data #7: Final particle stack for hdMSP-1 conformation 2 [picked particles - single frame - processed] Data #8: Final particle stack for MSP-1 main conformation [picked particles - single frame - processed] Data #9: Final particle stack for MSP-1 alternative conformation 1 [picked particles - single frame - processed] Data #10: Final particle stack for MSP-1 alternative conformation 2 [picked particles - single frame - processed] Data #11: Final particle stack for MSP-1 alternative conformation 3 [picked particles - single frame - processed] Data #12: Final particle stack for MSP-1 alternative conformation 4 [picked particles - single frame - processed] Data #13: Final particle stack for MSP-1 alternative conformation 5 [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unfiltered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Additional map: Sharpened map
+Additional map: Focused refinement coiled-coil domain, unfiltered
+Additional map: Focused refinement wing domain, sharpened
+Additional map: Focused refinement wing domain, unfiltered
+Additional map: Focused refinement coiled-coil domain, sharpened
+Additional map: Sharpened map (DeepEMhancer)
+Additional map: Focused refinement wing domain, sharpened (DeepEMhancer)
+Half map: #2
+Half map: #1
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Sample components
-Entire : Merozoite surface protein 1 (MSP-1)
Entire | Name: Merozoite surface protein 1 (MSP-1) |
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Components |
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-Supramolecule #1: Merozoite surface protein 1 (MSP-1)
Supramolecule | Name: Merozoite surface protein 1 (MSP-1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Heteromeric assembly of p83/30 fusion and p38/42 fusion of MSP-1 from Plasmodium falciparum (monomer), processed with SUB-1 protease into the MSP-1 complex composed of the subunits p83, p30, p38, and p42 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Merozoite surface antigens
Macromolecule | Name: Merozoite surface antigens / type: protein_or_peptide / ID: 1 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 81.773539 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VTHESYQELV KKLEALEDAV LTGYSLFQKE KMVLNEEEIT TKGASAQSGA SAQSGASAQS GASAQSGASA QSGASAQSGT SGPSGPSGT SPSSRSNTLP RSNTSSGASP PADASDSDAK SYADLKHRVR NYLFTIKELK YPELFDLTNH MLTLCDNIHG F KYLIDGYE ...String: VTHESYQELV KKLEALEDAV LTGYSLFQKE KMVLNEEEIT TKGASAQSGA SAQSGASAQS GASAQSGASA QSGASAQSGT SGPSGPSGT SPSSRSNTLP RSNTSSGASP PADASDSDAK SYADLKHRVR NYLFTIKELK YPELFDLTNH MLTLCDNIHG F KYLIDGYE EINELLYKLN FYFDLLRAKL NDVCANDYCQ IPFNLKIRAN ELDVLKKLVF GYRKPLDNIK DNVGKMEDYI KK NKTTIAN INELIEGSKK TIDQNKNADN EEGKKKLYQA QYDLSIYNKQ LEEAHNLISV LEKRIDTLKK NENIKKLLDK INE IKNPPP ANSGNTPNTL LDKNKKIEEH EEKIKEIAKT IKFNIDSLFT DPLELEYYLR EKNKKVDVTP KSQDPTKSVQ IPKV PYPNG IVYPLPLTDI HNSLAADNDK NSYGDLMNPH TKEKINEKII TDNKERKIFI NNIKKKIDLE EKNINHTKEQ NKKLL EDYE KSKKDYEELL EKFYEMKFNN NFDKDVVDKI FSARYTYNVE KQRYNNKFSS SNNSVYNVQK LKKALSYLED YSLRKG ISE KDFNHYYTLK TGLEADIKKL TEEIKSSENK ILEKNFKGLT HSANGSLEVS DIVKLQVQKV LLIKKIEDLR KIELFLK NA QLKDSIHVPN IYKPQNKPEP YYLIVLKKEV DKLKEFIPKV KDMLKKEQAV LSSITQPLVA ASETTEDGGH STHTL |
-Macromolecule #2: Merozoite surface antigens
Macromolecule | Name: Merozoite surface antigens / type: protein_or_peptide / ID: 2 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.217637 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SQSGETEVTE ETEETEETVG HTTTVTITLP PTQPSPPKEV KVVENSIEQK SNDNSQALTK TVYLKKLDEF LTKSYICHKY ILVSNSSMD QKLLEVYNLT PEEENELKSC DPLDLLFNIQ NNIPAMYSLY DSMNNDLQHL FFELYQKEMI YYLHKLKEEN H IKKLLEEQ KQITGT |
-Macromolecule #3: Merozoite surface protein-1
Macromolecule | Name: Merozoite surface protein-1 / type: protein_or_peptide / ID: 3 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.390676 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SSTSSPGNTT VNTAQSATHS NSQNQQSNAS STNTQNGVAV SSGPAVVEES HDPLTVLSIS NDLKGIVSLL NLGNKTKVPN PLTISTTEM EKFYENILKN NDTYFNDDIK QFVKSNSKVI TGLTETQKNA LNDEIKKLKD TLQLSFDLYN KYKLKLDRLF N KKKELGQD ...String: SSTSSPGNTT VNTAQSATHS NSQNQQSNAS STNTQNGVAV SSGPAVVEES HDPLTVLSIS NDLKGIVSLL NLGNKTKVPN PLTISTTEM EKFYENILKN NDTYFNDDIK QFVKSNSKVI TGLTETQKNA LNDEIKKLKD TLQLSFDLYN KYKLKLDRLF N KKKELGQD KMQIKKLTLL KEQLESKLNS LNNPHNVLQN FSVFFNKKKE AEIAETENTL ENTKILLKHY KGLVKYYNGE SS PLKTLSE VSIQTEDNYA NLEKFRVLSK IDGKLNDNLH LGKKKLSFLS SGLHHLITEL KEVIKNKNYT GNSPSENNKK VNE ALKSYE NFLPEAKVTT VVTPPQPDVT PSPLSVRVSG SSGSTKEETQ IPTSGSLLTE LQQVVQLQNY DEEDDSLVVL PIFG ESEDN DEYLDQVVTG E |
-Macromolecule #4: Merozoite surface protein 1
Macromolecule | Name: Merozoite surface protein 1 / type: protein_or_peptide / ID: 4 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.243133 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AISVTMDNIL SGFENEYDVI YLKPLAGVYR SLKKQIEKNI FTFNLNLNDI LNSRLKKRKY FLDVLESDLM QFKHISSNEY IIEDSFKLL NSEQKNTLLK SYKYIKESVE NDIKFAQEGI SYYEKVLAKY KDDLESIKKV IKEEKEKFPS SPPTTPPSPA K TDEQKKES ...String: AISVTMDNIL SGFENEYDVI YLKPLAGVYR SLKKQIEKNI FTFNLNLNDI LNSRLKKRKY FLDVLESDLM QFKHISSNEY IIEDSFKLL NSEQKNTLLK SYKYIKESVE NDIKFAQEGI SYYEKVLAKY KDDLESIKKV IKEEKEKFPS SPPTTPPSPA K TDEQKKES KFLPFLTNIE TLYNNLVNKI DDYLINLKAK INDCNVEKDE AHVKITKLSD LKAIDDKIDL FKNPYDFEAI KK LINDDTK KDMLGKLLST GLVQNFPNTI ISKLIEGKFQ DMLNISQHQC VKKQCPENSG CFRHLDEREE CKCLLNYKQE GDK CVENPN PTCNENNGGC DADATCTEED SGSSRKKITC ECTKPDSYPL FDGIFCSSSN |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
Details | Heteromeric assembly of p83/30 fusion and p38/42 fusion of MSP-1 from Plasmodium falciparum (monomer), processed with SUB-1 protease into the MSP-1 complex composed of the subunits p83, p30, p38, and p42 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |