+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13637 | ||||||||||||
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Title | In-situ structure of hexameric S-layer protein | ||||||||||||
Map data | Postprocessed map without B-factor sharpening. | ||||||||||||
Sample |
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Keywords | S-layer csg / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Surface glycoprotein signal peptide / Major cell surface glycoprotein / PGF-CTERM archaeal protein-sorting signal / PGF-CTERM motif / S-layer / cell wall organization / extracellular region / plasma membrane / Cell surface glycoprotein Function and homology information | ||||||||||||
Biological species | Haloferax volcanii DS2 (archaea) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.968 Å | ||||||||||||
Authors | von Kuegelgen A / Bharat TAM | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Cell Rep / Year: 2021 Title: Complete atomic structure of a native archaeal cell surface. Authors: Andriko von Kügelgen / Vikram Alva / Tanmay A M Bharat / Abstract: Many prokaryotic cells are covered by an ordered, proteinaceous, sheet-like structure called a surface layer (S-layer). S-layer proteins (SLPs) are usually the highest copy number macromolecules in ...Many prokaryotic cells are covered by an ordered, proteinaceous, sheet-like structure called a surface layer (S-layer). S-layer proteins (SLPs) are usually the highest copy number macromolecules in prokaryotes, playing critical roles in cellular physiology such as blocking predators, scaffolding membranes, and facilitating environmental interactions. Using electron cryomicroscopy of two-dimensional sheets, we report the atomic structure of the S-layer from the archaeal model organism Haloferax volcanii. This S-layer consists of a hexagonal array of tightly interacting immunoglobulin-like domains, which are also found in SLPs across several classes of archaea. Cellular tomography reveal that the S-layer is nearly continuous on the cell surface, completed by pentameric defects in the hexagonal lattice. We further report the atomic structure of the SLP pentamer, which shows markedly different relative arrangements of SLP domains needed to complete the S-layer. Our structural data provide a framework for understanding cell surfaces of archaea at the atomic level. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13637.map.gz | 24 MB | EMDB map data format | |
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Header (meta data) | emd-13637-v30.xml emd-13637.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_13637.png | 159.9 KB | ||
Masks | emd_13637_msk_1.map | 27 MB | Mask map | |
Filedesc metadata | emd-13637.cif.gz | 6.8 KB | ||
Others | emd_13637_additional_1.map.gz | 19.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13637 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13637 | HTTPS FTP |
-Validation report
Summary document | emd_13637_validation.pdf.gz | 529.2 KB | Display | EMDB validaton report |
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Full document | emd_13637_full_validation.pdf.gz | 528.8 KB | Display | |
Data in XML | emd_13637_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_13637_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13637 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13637 | HTTPS FTP |
-Related structure data
Related structure data | 7pttMC 7ptpC 7ptrC 7ptuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13637.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map without B-factor sharpening. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13637_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Full map without postprocessing or B-factor sharpening
File | emd_13637_additional_1.map | ||||||||||||
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Annotation | Full map without postprocessing or B-factor sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : In-situ structure of hexameric S-layer of Haloferax volcanii
Entire | Name: In-situ structure of hexameric S-layer of Haloferax volcanii |
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Components |
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-Supramolecule #1: In-situ structure of hexameric S-layer of Haloferax volcanii
Supramolecule | Name: In-situ structure of hexameric S-layer of Haloferax volcanii type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: In-situ structure of hexameric S-layer of Haloferax volcanii |
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Source (natural) | Organism: Haloferax volcanii DS2 (archaea) / Location in cell: Cell surface |
-Macromolecule #1: Cell surface glycoprotein
Macromolecule | Name: Cell surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloferax volcanii DS2 (archaea) |
Molecular weight | Theoretical: 81.755602 KDa |
Sequence | String: ERGNLDADSE SFNKTIQSGD RVFLGEEIST DAGLGASNPL LTGTAGNSEG VSLDLSSPIP QTTENQPLGT YDVDGSGSAT TPNVTLLAP RITDSEILTS SGGDVTGSAI SSSDAGNLYV NADYNYESAE KVEVTVEDPS GTDITNEVLS GTDTFVDDGS I GSTSSTGG ...String: ERGNLDADSE SFNKTIQSGD RVFLGEEIST DAGLGASNPL LTGTAGNSEG VSLDLSSPIP QTTENQPLGT YDVDGSGSAT TPNVTLLAP RITDSEILTS SGGDVTGSAI SSSDAGNLYV NADYNYESAE KVEVTVEDPS GTDITNEVLS GTDTFVDDGS I GSTSSTGG GVGIDMSDQD AGEYTIILEG AEDLDFGDAT ETMTLTISSQ DEIGIELDSE SVTQGTDVQY TVTNGIDGNE HV VAMDLSD LQNDATTEQA KEVFRNIGDT SEVGIANSSA TNTSGSSTGP TVETADIAYA VVEIDGASAV GGIETQYLDD SEV DLEVYD AGVSATAAVG QDATNDITLT IEEGGTTLSS PTGQYVVGSE VDINGTATSS DSVAIYVRDD GDWQLLEIGG DNEI SVDSD DTFEEEDIAL SGLSGDGSSI LSLTGTYRIG VIDASDADVG GDGSVDDSLT TSEFTSGVSS SNSIRVTDQA LTGQF TTIN GQVAPVETGT VDINGTASGA NSVLVIFVDE RGNVNYQEVS VDSDGTYDED DITVGLTQGR VTAHILSVGR DSAIGD GSL PSGPSNGATL NDLTGYLDTL DQNNNNGEQI NELIASETVD ETASDDLIVT ETFRLAESST SIDSIYPDAA EAAGINP VA TGETMVIAGS TNLKPDDNTI SIEVTNEDGT SVALEDTDEW NNDGQWMVEI DTTDFETGTF TVEADDGDNT DTVNVEVV S EREDTTTSSD NATDTTTTTD GPTETTTTAE PTETTEEPTE ETTTSSNTPG FGIAVALVAL VGAALLALRR EN UniProtKB: Cell surface glycoprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 18 % (w/v) artificial sea water | |||||||||||||||||||||
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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: 20 seconds, 15 mA | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV Details: Vitrobot options: Blot time 2.0 seconds, Blot force -15,1, Wait time 0 seconds, Drain time 0.5 seconds. | |||||||||||||||||||||
Details | Haloferax volcanii vesicles |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Spherical aberration corrector: not used / Chromatic aberration corrector: not used / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | SerialEM Hagen Scheme |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 2.9 e/Å2 / Details: Dose symmetric tilt scheme (Hagen et al, JSB) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number classes used: 5 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.968 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 53063 |
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Extraction | Number tomograms: 127 / Number images used: 83713 / Reference model: Ab initio / Method: RELION / Software - Name: RELION (ver. 3.1) / Details: RELION subtomogram averaging |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 3.1) / Details: 3D-Classification using RELION3.1 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Angle assignment was performed within RELION3.1 |
-Atomic model buiding 1
Details | Rigid body fit inside coot of D1-D6 domains and real space refinement with restraints of the original model obtained by single particle analysis in PHENIX. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Best Fit |
Output model | PDB-7ptt: |