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- EMDB-50632: Cryo-EM structure of the 'crown'less Bcs macrocomplex for E. coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-50632
TitleCryo-EM structure of the 'crown'less Bcs macrocomplex for E. coli cellulose secretion in non-saturating c-di-GMP (local)
Map dataDeep EMhancer-sharpened cryo-EM map of the 'crown'less Bcs macrocomplex for cellulose secretion in E. coli in non-saturating c-di-GMP (local)
Sample
  • Complex: Locally refined 'crown'less Bcs macrocomplex in non-saturating c-di-GMP from the E. coli cellulose secretion system
    • Protein or peptide: Cyclic di-GMP binding protein BcsE
    • Protein or peptide: Cell division protein
    • Protein or peptide: Protein YhjR
    • Protein or peptide: Cellulose synthase catalytic subunit [UDP-forming]
    • Protein or peptide: Cellulose biosynthesis protein BcsG
    • Protein or peptide: Cyclic di-GMP-binding protein
    • Protein or peptide: Cellulose biosynthesis protein BcsF
  • Ligand: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsBacterial cellulose secretion / MEMBRANE PROTEIN
Function / homology
Function and homology information


cellulose biosynthetic process / UDP-alpha-D-glucose metabolic process / cell division / plasma membrane
Similarity search - Function
Cellulose synthase operon protein BcsQ / Cellulose biosynthesis protein BcsQ / Cellulose synthase, subunit B / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cyclic di-GMP-binding protein / Cell division protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsAnso I / Krasteva PV
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)757507European Union
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system.
Authors: Itxaso Anso / Samira Zouhir / Thibault Géry Sana / Petya Violinova Krasteva /
Abstract: Bacterial cellulosic polymers constitute a prevalent class of biofilm matrix exopolysaccharides that are synthesized by several types of bacterial cellulose secretion (Bcs) systems, which include ...Bacterial cellulosic polymers constitute a prevalent class of biofilm matrix exopolysaccharides that are synthesized by several types of bacterial cellulose secretion (Bcs) systems, which include conserved cyclic diguanylate (c-di-GMP)-dependent cellulose synthase modules together with diverse accessory subunits. In E. coli, the biogenesis of phosphoethanolamine (pEtN)-modified cellulose relies on the BcsRQABEFG macrocomplex, encompassing inner-membrane and cytosolic subunits, and an outer membrane porin, BcsC. Here, we use cryogenic electron microscopy to shed light on the molecular mechanisms of BcsA-dependent recruitment and stabilization of a trimeric BcsG pEtN-transferase for polymer modification, and a dimeric BcsF-dependent recruitment of an otherwise cytosolic BcsERQ regulatory complex. We further demonstrate that BcsE, a secondary c-di-GMP sensor, can remain dinucleotide-bound and retain the essential-for-secretion BcsRQ partners onto the synthase even in the absence of direct c-di-GMP-synthase complexation, likely lowering the threshold for c-di-GMP-dependent synthase activation. Such activation-by-proxy mechanism could allow Bcs secretion system activity even in the absence of substantial intracellular c-di-GMP increase, and is reminiscent of other widespread synthase-dependent polysaccharide secretion systems where dinucleotide sensing and/or synthase stabilization are carried out by key co-polymerase subunits.
History
DepositionJun 12, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50632.png

Downloads & links

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Map

FileDownload / File: emd_50632.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeep EMhancer-sharpened cryo-EM map of the 'crown'less Bcs macrocomplex for cellulose secretion in E. coli in non-saturating c-di-GMP (local)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 419.5 Å		0.84 Å/pix.
x 500 pix.
= 419.5 Å		0.84 Å/pix.
x 500 pix.
= 419.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.0017767221 - 1.7456958
Average (Standard dev.)0.00058847404 (±0.014503919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 419.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50632_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened cryo-EM map of the 'crown'less Bcs macrocomplex...

Fileemd_50632_additional_1.map
AnnotationUnsharpened cryo-EM map of the 'crown'less Bcs macrocomplex for cellulose secretion in E. coli in non-saturating c-di-GMP (local)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the 'crown'less Bcs macrocomplex for cellulose...

Fileemd_50632_half_map_1.map
AnnotationHalf-map of the 'crown'less Bcs macrocomplex for cellulose secretion in E. coli in non-saturating c-di-GMP (local)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the 'crown'less Bcs macrocomplex for cellulose...

Fileemd_50632_half_map_2.map
AnnotationHalf-map of the 'crown'less Bcs macrocomplex for cellulose secretion in E. coli in non-saturating c-di-GMP (local)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Locally refined 'crown'less Bcs macrocomplex in non-saturating c-...

EntireName: Locally refined 'crown'less Bcs macrocomplex in non-saturating c-di-GMP from the E. coli cellulose secretion system
Components
  • Complex: Locally refined 'crown'less Bcs macrocomplex in non-saturating c-di-GMP from the E. coli cellulose secretion system
    • Protein or peptide: Cyclic di-GMP binding protein BcsE
    • Protein or peptide: Cell division protein
    • Protein or peptide: Protein YhjR
    • Protein or peptide: Cellulose synthase catalytic subunit [UDP-forming]
    • Protein or peptide: Cellulose biosynthesis protein BcsG
    • Protein or peptide: Cyclic di-GMP-binding protein
    • Protein or peptide: Cellulose biosynthesis protein BcsF
  • Ligand: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Locally refined 'crown'less Bcs macrocomplex in non-saturating c-...

SupramoleculeName: Locally refined 'crown'less Bcs macrocomplex in non-saturating c-di-GMP from the E. coli cellulose secretion system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Local refinement in the context of an assembled macrocomplex
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 990 KDa

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Macromolecule #1: Cyclic di-GMP binding protein BcsE

MacromoleculeName: Cyclic di-GMP binding protein BcsE / type: protein_or_peptide / ID: 1
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 60.967539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASWSHPQFE KGSMRDIVDP VFSIGISSLW DELRHMPAGG VWWFNVDRHE DAISLANQTI ASQAETAHVA VISMDSDPAK IFQLDDSQG PEKIKLFSML NHEKGLYYLT RDLQCSIDPH NYLFILVCAN NAWQNIPAER LRSWLDKMNK WSRLNHCSLL V INPGNNND ...String:
MASWSHPQFE KGSMRDIVDP VFSIGISSLW DELRHMPAGG VWWFNVDRHE DAISLANQTI ASQAETAHVA VISMDSDPAK IFQLDDSQG PEKIKLFSML NHEKGLYYLT RDLQCSIDPH NYLFILVCAN NAWQNIPAER LRSWLDKMNK WSRLNHCSLL V INPGNNND KQFSLLLEEY RSLFGLASLR FQGDQHLLDI AFWCNEKGVS ARQQLSVQQQ NGIWTLVQSE EAEIQPRSDE KR ILSNVAV LEGAPPLSEH WQLFNNNEVL FNEARTAQAA TVVFSLQQNA QIEPLARSIH TLRRQRGSAM KILVRENTAS LRA TDERLL LACGANMVIP WNAPLSRCLT MIESVQGQKF SRYVPEDITT LLSMTQPLKL RGFQKWDVFC NAVNNMMNNP LLPA HGKGV LVALRPVPGI RVEQALTLCR PNRTGDIMTI GGNRLVLFLS FCRINDLDTA LNHIFPLPTG DIFSNRMVWF EDDQI SAEL VQMRLLAPEQ WGMPLPLTQS SKPVINAEHD GRHWRRIPEP MRLLDDAVER SS

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Macromolecule #2: Cell division protein

MacromoleculeName: Cell division protein / type: protein_or_peptide / ID: 2
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 27.960832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVLGLQGVR GGVGTTTITA ALAWSLQMLG ENVLVVDACP DNLLRLSFNV DFTHRQGWAR AMLDGQDWRD AGLRYTSQLD LLPFGQLSI EEQENPQHWQ TRLSDICSGL QQLKASGRYQ WILIDLPRDA SQITHQLLSL CDHSLAIVNV DANCHIRLHQ Q ALPDGAHI ...String:
MAVLGLQGVR GGVGTTTITA ALAWSLQMLG ENVLVVDACP DNLLRLSFNV DFTHRQGWAR AMLDGQDWRD AGLRYTSQLD LLPFGQLSI EEQENPQHWQ TRLSDICSGL QQLKASGRYQ WILIDLPRDA SQITHQLLSL CDHSLAIVNV DANCHIRLHQ Q ALPDGAHI LINNFRIGSQ VQDDIYQLWL QSQRRLLPML IHRDEAMAEC LAAKQPVGEY RSDALAAEEI LTLANWCLLN YS GLKTPVG SKS

UniProtKB: Cell division protein

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Macromolecule #3: Protein YhjR

MacromoleculeName: Protein YhjR / type: protein_or_peptide / ID: 3
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 8.645541 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH HHAAGSNNNE PDTLPDPAIG YIFQNDIVAL KQAFSLPDID YADISQREQL AAALKRWPLL AEFAQQK

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Macromolecule #4: Cellulose synthase catalytic subunit [UDP-forming]

MacromoleculeName: Cellulose synthase catalytic subunit [UDP-forming] / type: protein_or_peptide / ID: 4
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 1 / Enantiomer: LEVO / EC number: cellulose synthase (UDP-forming)
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 104.015688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSILTRWLLI PPVNARLIGR YRDYRRHGAS AFSATLGCFW MILAWIFIPL EHPRWQRIRA EHKNLYPHIN ASRPRPLDPV RYLIQTCWL LIGASRKETP KPRRRAFSGL QNIRGRYHQW MNELPERVSH KTQHLDEKKE LGHLSAGARR LILGIIVTFS L ILALICVT ...String:
MSILTRWLLI PPVNARLIGR YRDYRRHGAS AFSATLGCFW MILAWIFIPL EHPRWQRIRA EHKNLYPHIN ASRPRPLDPV RYLIQTCWL LIGASRKETP KPRRRAFSGL QNIRGRYHQW MNELPERVSH KTQHLDEKKE LGHLSAGARR LILGIIVTFS L ILALICVT QPFNPLAQFI FLMLLWGVAL IVRRMPGRFS ALMLIVLSLT VSCRYIWWRY TSTLNWDDPV SLVCGLILLF AE TYAWIVL VLGYFQVVWP LNRQPVPLPK DMSLWPSVDI FVPTYNEDLN VVKNTIYASL GIDWPKDKLN IWILDDGGRE EFR QFAQNV GVKYIARTTH EHAKAGNINN ALKYAKGEFV SIFDCDHVPT RSFLQMTMGW FLKEKQLAMM QTPHHFFSPD PFER NLGRF RKTPNEGTLF YGLVQDGNDM WDATFFCGSC AVIRRKPLDE IGGIAVETVT EDAHTSLRLH RRGYTSAYMR IPQAA GLAT ESLSAHIGQR IRWARGMVQI FRLDNPLTGK GLKFAQRLCY VNAMFHFLSG IPRLIFLTAP LAFLLLHAYI IYAPAL MIA LFVLPHMIHA SLTNSKIQGK YRHSFWSEIY ETVLAWYIAP PTLVALINPH KGKFNVTAKG GLVEEEYVDW VISRPYI FL VLLNLVGVAV GIWRYFYGPP TEMLTVVVSM VWVFYNLIVL GGAVAVSVES KQVRRSHRVE MTMPAAIARE DGHLFSCT V QDFSDGGLGI KINGQAQILE GQKVNLLLKR GQQEYVFPTQ VARVMGNEVG LKLMPLTTQQ HIDFVQCTFA RADTWALWQ DSYPEDKPLE SLLDILKLGF RGYRHLAEFA PSSVKGIFRV LTSLVSWVVS FIPRRPERSE TAQPSDQALA QQGSARSSGR TGLEFEEFY PYDVPDYAAD YKDDDDKRS

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Macromolecule #5: Cellulose biosynthesis protein BcsG

MacromoleculeName: Cellulose biosynthesis protein BcsG / type: protein_or_peptide / ID: 5
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 59.687984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQFTQNTAM PSSLWQYWRG LSGWNFYFLV KFGLLWAGYL NFHPLLNLVF AAFLLMPLPR YSLHRLRHWI ALPIGFALFW HDTWLPGPE SIMSQGSQVA GFSTDYLIDL VTRFINWQMI GAIFVLLVAW LFLSQWIRIT VFVVAILLWL NVLTLAGPSF S LWPAGQPT ...String:
MTQFTQNTAM PSSLWQYWRG LSGWNFYFLV KFGLLWAGYL NFHPLLNLVF AAFLLMPLPR YSLHRLRHWI ALPIGFALFW HDTWLPGPE SIMSQGSQVA GFSTDYLIDL VTRFINWQMI GAIFVLLVAW LFLSQWIRIT VFVVAILLWL NVLTLAGPSF S LWPAGQPT TTVTTTGGNA AATVAATGGA PVVGDMPAQT APPTTANLNA WLNNFYNAEA KRKSTFPSSL PADAQPFELL VI NICSLSW SDIEAAGLMS HPLWSHFDIE FKNFNSATSY SGPAAIRLLR ASCGQTSHTN LYQPANNDCY LFDNLSKLGF TQH LMMGHN GQFGGFLKEV RENGGMQSEL MDQTNLPVIL LGFDGSPVYD DTAVLNRWLD VTEKDKNSRS ATFYNTLPLH DGNH YPGVS KTADYKARAQ KFFDELDAFF TELEKSGRKV MVVVVPEHGG ALKGDRMQVS GLRDIPSPSI TDVPVGVKFF GMKAP HQGA PIVIEQPSSF LAISDLVVRV LDGKIFTEDN VDWKKLTSGL HKQHRSPRTQ MQ

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Macromolecule #6: Cyclic di-GMP-binding protein

MacromoleculeName: Cyclic di-GMP-binding protein / type: protein_or_peptide / ID: 6
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 86.184383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRKLFWICA VAMGMSAFPS FMTQATPATQ PLINAEPAVA AQTEQNPQVG QVMPGVQGAD APVVAQNGPS RDVKLTFAQI APPPGSMVL RGINPNGSIE FGMRSDEVVT KAMLNLEYTP SPSLLPVQSQ LKVYLNDELM GVLPVTKEQL GKKTLAQMPI N PLFITDFN ...String:
MKRKLFWICA VAMGMSAFPS FMTQATPATQ PLINAEPAVA AQTEQNPQVG QVMPGVQGAD APVVAQNGPS RDVKLTFAQI APPPGSMVL RGINPNGSIE FGMRSDEVVT KAMLNLEYTP SPSLLPVQSQ LKVYLNDELM GVLPVTKEQL GKKTLAQMPI N PLFITDFN RVRLEFVGHY QDVCENPAST TLWLDVGRSS GLDLTYQTLN VKNDLSHFPV PFFDPRDNRT NTLPMVFAGA PD VGLQQAS AIVASWFGSR SGWRGQNFPV LYNQLPDRNA IVFATNDKRP DFLRDHPAVK APVIEMINHP QNPYVKLLVV FGR DDKDLL QAAKGIAQGN ILFRGESVVV NEVKPLLPRK PYDAPNWVRT DRPVTFGELK TYEEQLQSSG LEPAAINVSL NLPP DLYLM RSTGIDMDIN YRYTMPPVKD SSRMDISLNN QFLQSFNLSS KQEANRLLLR IPVLQGLLDG KTDVSIPALK LGATN QLRF DFEYMNPMPG GSVDNCITFQ PVQNHVVIGD DSTIDFSKYY HFIPMPDLRA FANAGFPFSR MADLSQTITV MPKAPN EAQ METLLNTVGF IGAQTGFPAI NLTVTDDGST IQGKDADIMI IGGIPDKLKD DKQIDLLVQA TESWVKTPMR QTPFPGI VP DESDRAAETR STLTSSGAMA AVIGFQSPYN DQRSVIALLA DSPRGYEMLN DAVNDSGKRA TMFGSVAVIR ESGINSLR V GDVYYVGHLP WFERLWYALA NHPILLAVLA AISVILLAWV LWRLLRIISR RRLNPDNE

UniProtKB: Cyclic di-GMP-binding protein

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Macromolecule #7: Cellulose biosynthesis protein BcsF

MacromoleculeName: Cellulose biosynthesis protein BcsF / type: protein_or_peptide / ID: 7
Details: Purified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 1094
Molecular weightTheoretical: 7.378975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MMTISDIIEI IVVCALIFFP LGYLARHSLR RIRDTLRLFF AKPRYVKPAG TLRRTEKARA TKK

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Macromolecule #8: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydr...

MacromoleculeName: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
type: ligand / ID: 8 / Number of copies: 4 / Formula: C2E
Molecular weightTheoretical: 690.411 Da
Chemical component information

ChemComp-C2E:
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration2 mg/mL
BufferpH: 8
Details: 120 mM NaCL 20 mM HEPES pH8 5 mM MgCl2 10 uM ApppCp 4 uM c-di-GMP 0.01% LM-NPG
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K
DetailsPurified Bcs macrocomplex with stoichiometry BcsA-BcsB6-BcsR2-BcsQ2-BcsE2-BcsF2-BcsG3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 20022 / Average electron dose: 49.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsGIF Quantum LS
Particle selectionNumber selected: 1359795
Startup modelType of model: INSILICO MODEL
In silico model: Ab-initio and 3D classification (cryoSPARC)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 314979
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

fold

source_name: Other, initial_model_type: in silico modelColabFold model for full-length BcsA-BcsG3 complex

6ybb

source_name: PDB, initial_model_type: experimental modelcrystal structure of the BcsERQ complex

fold

source_name: Other, initial_model_type: in silico modelColabFold model for full-length BcsE2-BcsF2 complex
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9fp0:
Cryo-EM structure of the 'crown'less Bcs macrocomplex for E. coli cellulose secretion in non-saturating c-di-GMP (local)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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