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- EMDB-0862: Esx-3 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-0862
TitleEsx-3
Map data
Sample
  • Complex: esx-3
    • Protein or peptide: ESX-3 secretion system ATPase EccB3
    • Protein or peptide: ESX-3 secretion system protein EccD3
    • Protein or peptide: ESX-3 secretion system protein EccC3
    • Protein or peptide: ESX-3 secretion system protein EccE3
KeywordsMembrane 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
: / Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain ...: / Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system ESX-1, transport TM domain B / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX-3 secretion system ATPase EccB3 / ESX-3 secretion system protein EccC3 / ESX-3 secretion system protein EccD3 / ESX-3 secretion system protein EccE3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang SH / Zhou KX
CitationJournal: To Be Published
Title: cryo-em structure of esx-3
Authors: Wang SH / Zhou KX / Li J / Rao ZH
History
DepositionNov 13, 2019-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lar
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0862.png

Downloads & links

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Map

FileDownload / File: emd_0862.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 360.8 Å		0.82 Å/pix.
x 440 pix.
= 360.8 Å		0.82 Å/pix.
x 440 pix.
= 360.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.035
Minimum - Maximum-0.113354094 - 0.17274204
Average (Standard dev.)0.00049343787 (±0.00405674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 360.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z360.800360.800360.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.1130.1730.000

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Supplemental data

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Sample components

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Entire : esx-3

EntireName: esx-3
Components
  • Complex: esx-3
    • Protein or peptide: ESX-3 secretion system ATPase EccB3
    • Protein or peptide: ESX-3 secretion system protein EccD3
    • Protein or peptide: ESX-3 secretion system protein EccC3
    • Protein or peptide: ESX-3 secretion system protein EccE3

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Supramolecule #1: esx-3

SupramoleculeName: esx-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: ESX-3 secretion system ATPase EccB3

MacromoleculeName: 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
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 53.684262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: ESX-3 secretion system protein EccD3

MacromoleculeName: ESX-3 secretion system protein EccD3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 48.29248 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: ESX-3 secretion system protein EccC3

MacromoleculeName: ESX-3 secretion system protein EccC3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 49.900879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #4: ESX-3 secretion system protein EccE3

MacromoleculeName: ESX-3 secretion system protein EccE3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 33.226992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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

Concentration5 mg/mL
BufferpH: 7.5 / Component:
ConcentrationFormula
20.0 mMHEPES
100.0 mMNaCl
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied 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 assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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