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- EMDB-37939: Open Falcilysin, from MK-4815-treated dataset -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37939
TitleOpen Falcilysin, from MK-4815-treated dataset
Map data
Sample
  • Complex: Falcilysin
    • Protein or peptide: Falcilysin
  • Ligand: ZINC ION
Keywordsfalcilysin open conformation / HYDROLASE
Function / homology
Function and homology information


hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / protein processing / metalloendopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M16C associated / Peptidase M16C associated / Peptidase M16C associated / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLin JQ / Yan XF / Lescar J
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Not funded Singapore
CitationJournal: To Be Published
Title: Open Falcilysin, from MK-4815-treated dataset
Authors: Lin JQ / Yan XF / Lescar J
History
DepositionOct 31, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37939.png

Downloads & links

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Map

FileDownload / File: emd_37939.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 128 pix.
= 148.48 Å		1.16 Å/pix.
x 128 pix.
= 148.48 Å		1.16 Å/pix.
x 128 pix.
= 148.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.027265707 - 0.06238814
Average (Standard dev.)0.00009059821 (±0.0033878013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 148.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37939_msk_1.map
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Additional map: #2

Fileemd_37939_additional_1.map
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Additional map: #1

Fileemd_37939_additional_2.map
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Half map: #2

Fileemd_37939_half_map_1.map
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Half map: #1

Fileemd_37939_half_map_2.map
Projections & Slices
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Sample components

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Entire : Falcilysin

EntireName: Falcilysin
Components
  • Complex: Falcilysin
    • Protein or peptide: Falcilysin
  • Ligand: ZINC ION

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Supramolecule #1: Falcilysin

SupramoleculeName: Falcilysin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Macromolecule #1: Falcilysin

MacromoleculeName: Falcilysin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 132.034156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IHEKSPKHNS YDIIEKRYNE EFKMTYTVYQ HKKAKTQVIS LGTNDPLDVE QAFAFYVKTL THSGKGIPHI LEHSVLSGSK NYNYKNSIG LLEKGTLHTH LNAYTFNDRT VYMAGSMNNK DFFNIMGVYM DSVFQPNVLE NKYIFETEGW TYEVEKLKED E KGKAEIPQ ...String:
IHEKSPKHNS YDIIEKRYNE EFKMTYTVYQ HKKAKTQVIS LGTNDPLDVE QAFAFYVKTL THSGKGIPHI LEHSVLSGSK NYNYKNSIG LLEKGTLHTH LNAYTFNDRT VYMAGSMNNK DFFNIMGVYM DSVFQPNVLE NKYIFETEGW TYEVEKLKED E KGKAEIPQ MKDYKVSFNG IVYNEMKGAL SSPLEDLYHE EMKYMFPDNV HSNNSGGDPK EITNLTYEEF KEFYYKNYNP KK VKVFFFS KNNPTELLNF VDQYLGQLDY SKYRDDAVES VEYQTYKKGP FYIKKKYGDH SEEKENLVSV AWLLNPKVDK TNN HNNNHS NNQSSENNGY SNGSHSSDLS LENPTDYFVL LIINNLLIHT PESVLYKALT DCGLGNNVID RGLNDSLVQY IFSI GLKGI KRNNEKIKNF DKVHYEVEDV IMNALKKVVK EGFNKSAVEA SINNIEFILK EANLKTSKSI DFVFEMTSKL NYNRD PLLI FEFEKYLNIV KNKIKNEPMY LEKFVEKHFI NNAHRSVILL EGDENYAQEQ ENLEKQELKK RIENFNEQEK EQVIKN FEE LSKYKNAEES PEHLNKFPII SISDLNKKTL EVPVNVYFTN INENNNIMET YNKLKTNEHM LKDNMDVFLK KYVLKND KH NTNNNNNNNN NMDYSFTETK YEGNVPILVY EMPTTGIVYL QFVFSLDHLT VDELAYLNLF KTLILENKTN KRSSEDFV I LREKNIGSMS ANVALYSKDD HLNVTDKYNA QALFNLEMHV LSHKCNDALN IALEAVKESD FSNKKKVIDI LKRKINGMK TTFSEKGYAI LMKYVKAHLN SKHYAHNIIY GYENYLKLQE QLELAENDFK TLENILVRIR NKIFNKKNLM VSVTSDYGAL KHLFVNSNE SLKNLVSYFE ENDKYINDMQ NKVNDPTVMG WNEEIKSKKL FDEEKVKKEF FVLPTFVNSV SMSGILFKPG E YLDPSFTV IVAALKNSYL WDTVRGLNGA YGVFADIEYD GSVVFLSARD PNLEKTLATF RESAKGLRKM ADTMTENDLL RY IINTIGT IDKPRRGIEL SKLSFLRLIS NESEQDRVEF RKRIMNTKKE DFYKFADLLE SKVNEFEKNI VIITTKEKAN EYI ANVDGE FKKVLIE

UniProtKB: Falcilysin

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / 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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45566
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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