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- EMDB-20333: CryoEM Plasmodium falciparum M18 aspartyl aminopeptidase -

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Basic information

Entry
Database: EMDB / ID: EMD-20333
TitleCryoEM Plasmodium falciparum M18 aspartyl aminopeptidase
Map dataPlasmodium falciparum M18
Sample
  • Complex: Plasmodium falciparum M18 aspartyl aminopeptidase
    • Protein or peptide: M18 aspartyl aminopeptidase
  • Ligand: ZINC ION
Function / homologyPeptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / aminopeptidase activity / metallopeptidase activity / zinc ion binding / M18 aspartyl aminopeptidase
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Plasmodium falciparum (isolate NF54) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHo C / Zhou ZH
Funding support United States, 10 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM071940 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)DE025567 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)AI094386 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U24GM116792 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007323 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99/R00 HL133453 United States
CitationJournal: Nat Methods / Year: 2020
Title: Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu.
Authors: Chi-Min Ho / Xiaorun Li / Mason Lai / Thomas C Terwilliger / Josh R Beck / James Wohlschlegel / Daniel E Goldberg / Anthony W P Fitzpatrick / Z Hong Zhou /
Abstract: X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up ...X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.
History
DepositionJun 21, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseDec 11, 2019-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.108
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.108
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pev
  • Surface level: 0.108
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20333.png

Downloads & links

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Map

FileDownload / File: emd_20333.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium falciparum M18
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.108 / Movie #1: 0.108
Minimum - Maximum-0.18047863 - 0.31202805
Average (Standard dev.)0.0005793639 (±0.011046562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1800.3120.001

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Supplemental data

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Sample components

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Entire : Plasmodium falciparum M18 aspartyl aminopeptidase

EntireName: Plasmodium falciparum M18 aspartyl aminopeptidase
Components
  • Complex: Plasmodium falciparum M18 aspartyl aminopeptidase
    • Protein or peptide: M18 aspartyl aminopeptidase
  • Ligand: ZINC ION

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Supramolecule #1: Plasmodium falciparum M18 aspartyl aminopeptidase

SupramoleculeName: Plasmodium falciparum M18 aspartyl aminopeptidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: M18 aspartyl aminopeptidase

MacromoleculeName: M18 aspartyl aminopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate NF54) (eukaryote) / Strain: isolate NF54
Molecular weightTheoretical: 65.72193 KDa
SequenceString: MDKKAREYAQ DALKFIQRSG SNFLACKNLK ERLENNGFIN LSEGETWNLN KNEGYVLCKE NRNICGFFVG KNFNIDTGSI LISIGHIDS CALKISPNNN VIKKKIHQIN VECYGSGLWH TWFDRSLGLS GQVLYKKGNK LVEKLIQINK SVLFLPSLAI H LQNRTRYD ...String:
MDKKAREYAQ DALKFIQRSG SNFLACKNLK ERLENNGFIN LSEGETWNLN KNEGYVLCKE NRNICGFFVG KNFNIDTGSI LISIGHIDS CALKISPNNN VIKKKIHQIN VECYGSGLWH TWFDRSLGLS GQVLYKKGNK LVEKLIQINK SVLFLPSLAI H LQNRTRYD FSVKINYENH IKPIISTTLF NQLNKCKRNN VHHDTILTTD TKFSHKENSQ NKRDDQMCHS FNDKDVSNHN LD KNTIEHL TNQQNEEKNK HTKDNPNSKD IVEHINTDNS YPLLYLLSKE LNCKEEDILD FELCLMDTQE PCFTGVYEEF IEG ARFDNL LGSFCVFEGF IELVNSIKNH TSNENTNHTN NITNDINDNI HNNLYISIGY DHEEIGSLSE VGARSYCTKN FIDR IISSV FKKEIHEKNL SVQEIYGNLV NRSFILNVDM AHCSHPNYPE TVQDNHQLFF HEGIAIKYNT NKNYVTSPLH ASLIK RTFE LYYNKYKQQI KYQNFMVKND TPCGSTVGSM VAANLSMPGI DIGIPQLAMH SIREIAAVHD VFFLIKGVFA FYTYYN QVL STCVHDK

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Number images used: 5860
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 1)

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