[English] 日本語
Yorodumi- EMDB-37938: Partially closed Falcilysin bound to MK-4815, from MK-4815-treate... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37938 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Partially closed Falcilysin bound to MK-4815, from MK-4815-treated dataset | |||||||||
Map data | map after 'auto-refine' in RELION, after 'Bayesian polishing' | |||||||||
Sample |
| |||||||||
Keywords | falcilysin partially closed conformation / MK-4815 binding / 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 | |||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Lin JQ / Yan XF / Lescar J | |||||||||
Funding support | Singapore, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Partially closed Falcilysin bound to MK-4815, from MK-4815-treated dataset Authors: Lin JQ / Yan XF / Lescar J | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_37938.map.gz | 6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-37938-v30.xml emd-37938.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37938_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_37938.png | 20.9 KB | ||
Masks | emd_37938_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-37938.cif.gz | 6.1 KB | ||
Others | emd_37938_additional_1.map.gz emd_37938_additional_2.map.gz emd_37938_half_map_1.map.gz emd_37938_half_map_2.map.gz | 7.5 MB 1.1 MB 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37938 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37938 | HTTPS FTP |
-Validation report
Summary document | emd_37938_validation.pdf.gz | 863.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_37938_full_validation.pdf.gz | 862.9 KB | Display | |
Data in XML | emd_37938_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_37938_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37938 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37938 | HTTPS FTP |
-Related structure data
Related structure data | 8wytMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_37938.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | map after 'auto-refine' in RELION, after 'Bayesian polishing' | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_37938_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: unmasked map from 'Post-processing' in RELION
File | emd_37938_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unmasked map from 'Post-processing' in RELION | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: masked map from 'Post-processing' in RELION
File | emd_37938_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | masked map from 'Post-processing' in RELION | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_37938_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_37938_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Falcilysin
Entire | Name: Falcilysin |
---|---|
Components |
|
-Supramolecule #1: Falcilysin
Supramolecule | Name: Falcilysin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
-Macromolecule #1: Falcilysin
Macromolecule | Name: Falcilysin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
---|---|
Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
Molecular weight | Theoretical: 135.039359 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHSSG VDLGTENLYF QSMEWIHEKS PKHNSYDIIE KRYNEEFKMT YTVYQHKKAK TQVISLGTND PLDVEQAFAF YVKTLTHSG KGIPHILEHS VLSGSKNYNY KNSIGLLEKG TLHTHLNAYT FNDRTVYMAG SMNNKDFFNI MGVYMDSVFQ P NVLENKYI ...String: MHHHHHHSSG VDLGTENLYF QSMEWIHEKS PKHNSYDIIE KRYNEEFKMT YTVYQHKKAK TQVISLGTND PLDVEQAFAF YVKTLTHSG KGIPHILEHS VLSGSKNYNY KNSIGLLEKG TLHTHLNAYT FNDRTVYMAG SMNNKDFFNI MGVYMDSVFQ P NVLENKYI FETEGWTYEV EKLKEDEKGK AEIPQMKDYK VSFNGIVYNE MKGALSSPLE DLYHEEMKYM FPDNVHSNNS GG DPKEITN LTYEEFKEFY YKNYNPKKVK VFFFSKNNPT ELLNFVDQYL GQLDYSKYRD DAVESVEYQT YKKGPFYIKK KYG DHSEEK ENLVSVAWLL NPKVDKTNNH NNNHSNNQSS ENNGYSNGSH SSDLSLENPT DYFVLLIINN LLIHTPESVL YKAL TDCGL GNNVIDRGLN DSLVQYIFSI GLKGIKRNNE KIKNFDKVHY EVEDVIMNAL KKVVKEGFNK SAVEASINNI EFILK EANL KTSKSIDFVF EMTSKLNYNR DPLLIFEFEK YLNIVKNKIK NEPMYLEKFV EKHFINNAHR SVILLEGDEN YAQEQE NLE KQELKKRIEN FNEQEKEQVI KNFEELSKYK NAEESPEHLN KFPIISISDL NKKTLEVPVN VYFTNINENN NIMETYN KL KTNEHMLKDN MDVFLKKYVL KNDKHNTNNN NNNNNNMDYS FTETKYEGNV PILVYEMPTT GIVYLQFVFS LDHLTVDE L AYLNLFKTLI LENKTNKRSS EDFVILREKN IGSMSANVAL YSKDDHLNVT DKYNAQALFN LEMHVLSHKC NDALNIALE AVKESDFSNK KKVIDILKRK INGMKTTFSE KGYAILMKYV KAHLNSKHYA HNIIYGYENY LKLQEQLELA ENDFKTLENI LVRIRNKIF NKKNLMVSVT SDYGALKHLF VNSNESLKNL VSYFEENDKY INDMQNKVND PTVMGWNEEI KSKKLFDEEK V KKEFFVLP TFVNSVSMSG ILFKPGEYLD PSFTVIVAAL KNSYLWDTVR GLNGAYGVFA DIEYDGSVVF LSARDPNLEK TL ATFRESA KGLRKMADTM TENDLLRYII NTIGTIDKPR RGIELSKLSF LRLISNESEQ DRVEFRKRIM NTKKEDFYKF ADL LESKVN EFEKNIVIIT TKEKANEYIA NVDGEFKKVL IE UniProtKB: Falcilysin |
-Macromolecule #2: 2-(aminomethyl)-3,5-ditert-butyl-phenol
Macromolecule | Name: 2-(aminomethyl)-3,5-ditert-butyl-phenol / type: ligand / ID: 2 / Number of copies: 1 / Formula: H8F |
---|---|
Molecular weight | Theoretical: 235.365 Da |
Chemical component information | ChemComp-H8F: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |