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Yorodumi- EMDB-16483: In vitro structure of the Nitrosopumilus maritimus S-layer - Two-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16483 | |||||||||
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Title | In vitro structure of the Nitrosopumilus maritimus S-layer - Two-fold symmetry (C2) | |||||||||
Map data | PostProcessed map with B-factor sharpening | |||||||||
Sample |
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Keywords | Nmar_1547 S-layer / STRUCTURAL PROTEIN | |||||||||
Function / homology | membrane / Uncharacterized protein Function and homology information | |||||||||
Biological species | Nitrosopumilus maritimus SCM1 (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.71 Å | |||||||||
Authors | von Kuegelgen A / Bharat T | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To Be Published Title: Membrane-less channels sieve cations in ammonia-oxidising marine archaea Authors: von Kuegelgen A / Cassidy CK / van Dorst S / Pagani LL / Ford Z / Loewe J / Stansfeld PJ / Bharat TAM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16483.map.gz | 114 MB | EMDB map data format | |
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Header (meta data) | emd-16483-v30.xml emd-16483.xml | 26.2 KB 26.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16483_fsc.xml | 22.4 KB | Display | FSC data file |
Images | emd_16483.png | 290 KB | ||
Masks | emd_16483_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-16483.cif.gz | 8.6 KB | ||
Others | emd_16483_additional_1.map.gz emd_16483_half_map_1.map.gz emd_16483_half_map_2.map.gz | 112.5 MB 113.7 MB 113.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16483 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16483 | HTTPS FTP |
-Related structure data
Related structure data | 8c8lMC 8c8kC 8c8mC 8c8nC 8c8oC 8c8rC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16483.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | PostProcessed map with B-factor sharpening | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.092 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16483_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Full map with out b-factor sharpening
File | emd_16483_additional_1.map | ||||||||||||
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Annotation | Full map with out b-factor sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_16483_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_16483_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nitrosopumilus maritimus S-layer
Entire | Name: Nitrosopumilus maritimus S-layer |
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Components |
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-Supramolecule #1: Nitrosopumilus maritimus S-layer
Supramolecule | Name: Nitrosopumilus maritimus S-layer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nitrosopumilus maritimus S-layer C2 symmetrised |
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Source (natural) | Organism: Nitrosopumilus maritimus SCM1 (archaea) / Strain: SCM1 / Location in cell: extracellular |
-Macromolecule #1: Cell surface protein
Macromolecule | Name: Cell surface protein / type: protein_or_peptide / ID: 1 / Details: In-vitro isolated S-layer / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Nitrosopumilus maritimus SCM1 (archaea) / Strain: SCM1 |
Molecular weight | Theoretical: 183.156 KDa |
Sequence | String: MNNEIGRKIT SLTLMTIMVA GGLTFAIPGV MPEAMAANAN LFVSAENSQF DNYMSGPQVI EVVVIDSDIN DTDEAKGEPD VTVNGKVLR MVQAVDGNWY GYFADRDQAQ IADSTATTAD SGLDFGVFCA SSSGTAALGF STTETDGIAI PITIANATAT G NGTQTGSS ...String: MNNEIGRKIT SLTLMTIMVA GGLTFAIPGV MPEAMAANAN LFVSAENSQF DNYMSGPQVI EVVVIDSDIN DTDEAKGEPD VTVNGKVLR MVQAVDGNWY GYFADRDQAQ IADSTATTAD SGLDFGVFCA SSSGTAALGF STTETDGIAI PITIANATAT G NGTQTGSS SGGAITTTCA ANTLDASTAN GTINVVREAK DPVAASGSVS VGQIGLKNGT ANSGPNWPFI QLYELNPTGN VV VQYNKGG GVQSTTLTFD TVDQFAELSL DRTVFPRVSQ VHATITDLWL NIDPTDEDSW TFATNTKNTT SSFNVDTFYQ VFD ENGASG GSALTLRTTL SSLMCEDNCV LTLDVDAQSS GTPVVTIQDN GDSILTQLNA SSNTNANNAS AFGISTETAK LGTG SIPVT ITEQGPNSGV FGTYDESDKS VLKITDNAKR GTSASLDYNE TPQTILVGFS FASIDIQPVT DEWTSGQEIP VVIVD ADQN KNSRADEDLD LNNPDVTLIP ALRTGDPFTI DEGGTPSLIF TNGTNGDDSI FDTGAINNTS AGQVGNFTLN INVTRF SSA TNITSTESID TFSKRLISAQ TANSSANFDV DFAIIDLGSA TLETLKETVV DEDNTAVGFN FFNYDVRSLG ADTVSIA LL NTTGNILPWV NNDTRNVDKN NAILLVSNST NSQAYVDLTN AVSDAVYGST NTDSNVNIGF AMYFTGVGDL AAKEVIVM D FFSFGFTDDG VQSSERFANQ IIRIEAEETG DNTSTFEGSL EYVMVNQINI QDAGTFSGIT PIADDPSFIV IEDLTDEDA PRVNYNDLGA DGVTTPVSDQ EEAPSHSGVV SLNADSYKIA DTVVITVEDL DLNVDSDLID IFTVVSDNSK ATDDAVGSAT TQSLSFGEL GRLLDVTFDD VIWSTPDGAN NTATGNDSDT CSTELSNAGI TDTGLGATGF TLVETGAATG VFVGDFQIPS F WCRVSDTT TTPYTYAGDE ETTTGLDIEV NYVDFRDASG EIVEVGDSAG VRANTGSVSL DRTVYPVPFG TIADSSKAAN AA PNGRSVF PIHATGITST IDSTEELPTG DLTIHVRIND PDFDENPAGE DAMDQDNALK ISVIRGSDSV VLGYAGASER TGK IDVGGN NGTISNIRSF GEMDEIAPDA GIFELDVNIK FTDGPASAQC NSHDTLYTAL DGTTGKADTN RFDDGAASGQ EYCI LQGDI LQVEYTDPAD ASGDANTVTD SATFDLRNGV LQSDKSVYII GSDMILTLIE PDFDLDNDSA ETYDLDLIEW DSDAA TTTM GNKGVTGAAA AFDPEPTDFR ETGDSTGIFQ IVIEIPESLS NDKLERGEEI ILEYTDWGPS GSDYVGDEDE DVNLTI YTS NFGATVELDQ KVYSWTDKVY ITIVAPDHNF DSDLVDEIGE TDSDPIKVST RGFDLDNYKL VETGTDTGIF TGEVILT GF TAHDADGDGN TGDATGTTSG SGPTDGLLAT DDDDGLTVSF EFSEDETIVG SALIRWNIGE VQWLEASYPA SGTGVVRV I DPDMNLDPEA VDNFEVDVWS DSDAGGIDLT VTETNEATGI FEGTVFFTTL DESSGHRLRV SEGDTVTAEY EDNTLPDPY TTADELDITA TSLIGTVVPP LERAPAANLR TVDAFGNSLD SVSVDQQVQI SADLANGQDR EQSFAYLVQI QDANGVTVSL AWITGSLSS GQSFSPALSW IPTEAGTYTA TAFVWESVDN PTALSPPVST TVNVS UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 50 mM HEPES/NaOH pH=7.5, 500 mM NaCl, 50 mM MgCl2, 10 mM CaCl2 | |||||||||||||||
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA | |||||||||||||||
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV Details: absorption for 60 sec and blotted for 5 sec with blot force -10. | |||||||||||||||
Details | In vitro isolate S-layer cell envelopes |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 2.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000 |
Specialist optics | Spherical aberration corrector: not used / Chromatic aberration corrector: not used / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 12557 / Average exposure time: 4.2 sec. / Average electron dose: 48.5 e/Å2 Details: collected over three sessions with one session with the stage tilted by 33 degrees (alpha tilt) |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 41.4 / Target criteria: Best Fit |
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Output model | PDB-8c8l: |