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- EMDB-45766: CryoEM structure of the APO-BAM complex in SMA nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-45766
TitleCryoEM structure of the APO-BAM complex in SMA nanodisc
Map data
Sample
  • Complex: BamABCDE complex
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamB
    • Protein or peptide: Outer membrane protein assembly factor BamC
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamE
Keywordsmembrane protein / protein structure
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / identical protein binding / membrane
Similarity search - Function
Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / Outer membrane protein assembly factor BamE domain ...Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / Outer membrane protein assembly factor BamE domain / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Pyrrolo-quinoline quinone beta-propeller repeat / Omp85 superfamily domain / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSun D / Tegunov D / Payandeh J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: The discovery and structural basis of two distinct state-dependent inhibitors of BamA.
Authors: Dawei Sun / Kelly M Storek / Dimitry Tegunov / Ying Yang / Christopher P Arthur / Matthew Johnson / John G Quinn / Weijing Liu / Guanghui Han / Hany S Girgis / Mary Kate Alexander / Austin K ...Authors: Dawei Sun / Kelly M Storek / Dimitry Tegunov / Ying Yang / Christopher P Arthur / Matthew Johnson / John G Quinn / Weijing Liu / Guanghui Han / Hany S Girgis / Mary Kate Alexander / Austin K Murchison / Stephanie Shriver / Christine Tam / Hiroshi Ijiri / Hiroko Inaba / Tatsuya Sano / Hayato Yanagida / Junichi Nishikawa / Christopher E Heise / Wayne J Fairbrother / Man-Wah Tan / Nicholas Skelton / Wendy Sandoval / Benjamin D Sellers / Claudio Ciferri / Peter A Smith / Patrick C Reid / Christian N Cunningham / Steven T Rutherford / Jian Payandeh /
Abstract: BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of ...BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
History
DepositionJul 15, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45766.png

Downloads & links

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Map

FileDownload / File: emd_45766.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.661 Å		1.2 Å/pix.
x 256 pix.
= 307.661 Å		1.2 Å/pix.
x 256 pix.
= 307.661 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2018 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.218
Minimum - Maximum-1.2546142 - 2.030529
Average (Standard dev.)0.0012647888 (±0.03252722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.6608 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45766_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45766_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45766_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BamABCDE complex

EntireName: BamABCDE complex
Components
  • Complex: BamABCDE complex
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamB
    • Protein or peptide: Outer membrane protein assembly factor BamC
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamE

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Supramolecule #1: BamABCDE complex

SupramoleculeName: BamABCDE complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #5, #2-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 90.643383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV ...String:
MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV FQEGVSAEIQ QINIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NI DSTQVSL TPDKKGIYVT VNITEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYP RVQSMP EINDADKTVK LRVNVDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDT DTQRV PGSPDQVDVV YKVKERNTGS FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTV DGVS LGGRLFYNDF QADDADLSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSD QDN SFKTDDFTFN YGWTYNKLDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDG LG GKEMPFYENF YAGGSSTVRG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFIT P TPFISDKYAN SVRTSFFWDM GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAE QFQFNIGKTW

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.875277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ ...String:
MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ GYQQAVTVKL LNLEQAGKPV ADAASMQRYS TEMMNVISAG LDKSATDAAN AAQNRASTTM DVQSAADDTG LP MLVVRGP FNVVWQRLPA ALEKVGMKVT DSTRSQGNMA VTYKPLSDSD WQELGASDPG LASGDYKLQV GDLDNRSSLQ FID PKGHTL TQSQNDALVA VFQAAFSK

UniProtKB: Outer membrane protein assembly factor BamC

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Macromolecule #3: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.85835 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV ...String:
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV FLKDRLAKYE YSVAEYYTER GAWVAVVNRV EGMLRDYPDT QATRDALPLM ENAYRQMQMN AQAEKVAKII AA NSSNT

UniProtKB: Outer membrane protein assembly factor BamD

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Macromolecule #4: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.530256 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGNGGHHHH HHHH

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #5: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.918945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN ...String:
MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN GQLQALNEAD GAVKWTVNLD MPSLSLRGES APTTAFGAAV VGGDNGRVSA VLMEQGQMIW QQRISQATGS TE IDRLSDV DTTPVVVNGV VFALAYNGNL TALDLRSGQI MWKRELGSVN DFIVDGNRIY LVDQNDRVMA LTIDGGVTLW TQS DLLHRL LTSPVLYNGN LVVGDSEGYL HWINVEDGRF VAQQKVDSSG FQTEPVAADG KLLIQAKDGT VYSITR

UniProtKB: Outer membrane protein assembly factor BamB

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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