+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0862 | |||||||||
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Title | Esx-3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Membrane protein | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Wang SH / Zhou KX | |||||||||
Citation | Journal: To Be Published Title: cryo-em structure of esx-3 Authors: Wang SH / Zhou KX / Li J / Rao ZH | |||||||||
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_0862.map.gz | 303.5 MB | EMDB map data format | |
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Header (meta data) | emd-0862-v30.xml emd-0862.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_0862.png | 169.6 KB | ||
Filedesc metadata | emd-0862.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0862 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0862 | HTTPS FTP |
-Validation report
Summary document | emd_0862_validation.pdf.gz | 388.5 KB | Display | EMDB validaton report |
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Full document | emd_0862_full_validation.pdf.gz | 388.1 KB | Display | |
Data in XML | emd_0862_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_0862_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0862 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0862 | HTTPS FTP |
-Related structure data
Related structure data | 6larMC 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_0862.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : esx-3
Entire | Name: esx-3 |
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Components |
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-Supramolecule #1: esx-3
Supramolecule | Name: esx-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Macromolecule #1: ESX-3 secretion system ATPase EccB3
Macromolecule | Name: ESX-3 secretion system ATPase EccB3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 53.684262 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTGPVNPDDR RSFSSRTPVN ENPDGVQYRR GFVTRHQVSG WRFVMRRIAS GVALHDTRML VDPLRTQSRA VLTGALILVT GLVGCFIFS LFRPGGVPGN NAILADRSTS ALYVRVGEQL HPVLNLTSAR LISGSPDNPT MVKTSEIDKF PRGNLLGIPG A PERMVQNA ...String: MTGPVNPDDR RSFSSRTPVN ENPDGVQYRR GFVTRHQVSG WRFVMRRIAS GVALHDTRML VDPLRTQSRA VLTGALILVT GLVGCFIFS LFRPGGVPGN NAILADRSTS ALYVRVGEQL HPVLNLTSAR LISGSPDNPT MVKTSEIDKF PRGNLLGIPG A PERMVQNA ATDAEWTVCD AVGGANPGVT VIAGPLGADG ERAAPLPPDH AVLVHSDAEP NPGDWLLWDG KRSPIDLADR AV TDALGLG GQALAPRPIA AGLFNAVPAA PALTAPVIPD AGAAPQFELS LPVPVGAVVV AYDADNTARY YAVLSDGLQP ISP VLAAIL RNTDSHGFAQ PPRLGPDEVA RTPMSRGLDT SAYPDNPVTL VEASAHPVTC AHWTKPSDAA ESSLSVLSGA VLPL AEGLH TVDLVGAGAG GAANRVALTP GTGYFVQTVG AEPGSPTAGS MFWVSDTGVR YGIDTAEDDK VVAALGLSTS PLPVP WSVL SQFAAGPALS RGDALVAHDA VSTNPNSARM EASR UniProtKB: ESX-3 secretion system ATPase EccB3 |
-Macromolecule #2: ESX-3 secretion system protein EccD3
Macromolecule | Name: ESX-3 secretion system protein EccD3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 48.29248 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSENTVMPIV RVAVLAAGDD GGRLTEMALP SELPLREILP AVQRIVQPAR ENDGAADPAA APNPVRLSLA PIGGAPFSLD ATLDTVGVV DGDLLALQAV PSGPPAPRIV EDIADAAVIF SEARRRQWGP THIARGAALA LIGLILVGTG LSVAHRVITG D LLGQFIVS ...String: MSENTVMPIV RVAVLAAGDD GGRLTEMALP SELPLREILP AVQRIVQPAR ENDGAADPAA APNPVRLSLA PIGGAPFSLD ATLDTVGVV DGDLLALQAV PSGPPAPRIV EDIADAAVIF SEARRRQWGP THIARGAALA LIGLILVGTG LSVAHRVITG D LLGQFIVS GIALATVIAA LAVRNRSAVL ATSLAVTALV PVAAAFALGV PGDFGAPNVL LAAAGVAAWS LISMAGSPDD RG IAVFTAT AVTGVGVLLV AGAASLWVIS SDVIGCALVL LGLIVTVQAA QLSAMWARFP LPVIPAPGDP TPAARPLSVL ADL PRRVRV SQAHQTGVIA AGVLLGVAGS VALVSSANAS PWAWYIVVAA AAGAALRARV WDSAACKAWL LGHSYLLAVA LLVA FVIGD RYQAALWALA ALAVLVLVWI VAALNPKIAS PDTYSLPMRR MVGFLATGLD ASLIPVMALL VGLFSLVLDR UniProtKB: ESX-3 secretion system protein EccD3 |
-Macromolecule #3: ESX-3 secretion system protein EccC3
Macromolecule | Name: ESX-3 secretion system protein EccC3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 49.900879 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSRLIFEHQR RLTPPTTRKG TITIEPPPQL PRVVPPSLLR RVLPFLIVIL IVGMIVALFA TGMRLISPTM LFFPFVLLLA ATALYRGGD NKMRTEEVDA ERADYLRYLS VVRDNVRAHA AEQRAALEWS HPEPEVLATI PGTRRQWERD PRDRDFLVLR A GRHDVPLD ...String: MSRLIFEHQR RLTPPTTRKG TITIEPPPQL PRVVPPSLLR RVLPFLIVIL IVGMIVALFA TGMRLISPTM LFFPFVLLLA ATALYRGGD NKMRTEEVDA ERADYLRYLS VVRDNVRAHA AEQRAALEWS HPEPEVLATI PGTRRQWERD PRDRDFLVLR A GRHDVPLD AALKVKDTAD EIDLEPVAHS ALRGLLDVQR TVRDAPTGLD VAKLARITVI GEADEARAAI RAWIAQAVTW HD PTMLGVA LAAPDLESGD WSWLKWLPHV DVPNEADGVG PARYLTTSTA ELRERLAPAL ADRPLFPAES GAALKHLLVV LDD PDADPD DIARKPGLTG VTVIHRTTEL PNREQYPDPE RPILRVADGR IERWQVGGWQ PCVDVADAMS AAEAAHIARR LSRW DSNPG YIRSTSTGSA TFTTLLGIPD ASALDVHLGG IKAFHHHHHH HHHH UniProtKB: ESX-3 secretion system protein EccC3 |
-Macromolecule #4: ESX-3 secretion system protein EccE3
Macromolecule | Name: ESX-3 secretion system protein EccE3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 33.226992 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTARIALASL FVVAAVLAQP WQTTTQRWVL GVSIAAVIVL LAWWKGMFLT TRIGRALAMV RRNRAEDTVE TDAHRATVVL RVDPAAPAQ LPVVVGYLDR YGITCDKVRI THRDAGGTRR SWISLTVDAV DNLAALQARS ARIPLQDTTE VVGRRLADHL R EQGWTVTV ...String: MTARIALASL FVVAAVLAQP WQTTTQRWVL GVSIAAVIVL LAWWKGMFLT TRIGRALAMV RRNRAEDTVE TDAHRATVVL RVDPAAPAQ LPVVVGYLDR YGITCDKVRI THRDAGGTRR SWISLTVDAV DNLAALQARS ARIPLQDTTE VVGRRLADHL R EQGWTVTV VEGVDTPLPV SGKETWRGVA DDAGVVAAYR VKVDDRLDEV LAEIGHLPAE ETWTALEFTG SPAEPLLTVC AA VRTSDRP AAKAPLAGLT PARGRHRPAL AALNPLSTER LDGTAVPLPA VVRTSVKGSV EHEAAQEAGH PA UniProtKB: ESX-3 secretion system protein EccE3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||
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Buffer | pH: 7.5 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 25 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4823 / Average exposure time: 3.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000 |
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
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215839 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |