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- EMDB-39742: Cryo-EM structure of Escherichia coli OppBCDF in the resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-39742
TitleCryo-EM structure of Escherichia coli OppBCDF in the resting state
Map data
Sample
  • Complex: OppBCDF heterotetramer
    • Protein or peptide: Oligopeptide transport system permease protein OppB
    • Protein or peptide: Oligopeptide transport system permease protein OppC
    • Protein or peptide: Oligopeptide transport ATP-binding protein OppD
    • Protein or peptide: Oligopeptide transport ATP-binding protein OppF
  • Ligand: IRON/SULFUR CLUSTER
KeywordsABC importer / oligopeptide transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


peptidoglycan-associated peptide transport / oligopeptide import across plasma membrane / peptidoglycan peptide transmembrane transporter activity / ABC-type oligopeptide transporter / tripeptide import across plasma membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like ...: / Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Oligopeptide transport system permease protein OppB / Oligopeptide transport system permease protein OppC / Oligopeptide transport ATP-binding protein OppD / Oligopeptide transport ATP-binding protein OppF
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsLi P / Huang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Cryo-EM structure of Escherichia coli OppBCDF in the resting state
Authors: Li P / Huang Y
History
DepositionApr 12, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39742.png

Downloads & links

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Map

FileDownload / File: emd_39742.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 512 pix.
= 266.24 Å		0.52 Å/pix.
x 512 pix.
= 266.24 Å		0.52 Å/pix.
x 512 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0016853233 - 2.8093698
Average (Standard dev.)0.0012334933 (±0.026506731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39742_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_39742_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 : OppBCDF heterotetramer

EntireName: OppBCDF heterotetramer
Components
  • Complex: OppBCDF heterotetramer
    • Protein or peptide: Oligopeptide transport system permease protein OppB
    • Protein or peptide: Oligopeptide transport system permease protein OppC
    • Protein or peptide: Oligopeptide transport ATP-binding protein OppD
    • Protein or peptide: Oligopeptide transport ATP-binding protein OppF
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: OppBCDF heterotetramer

SupramoleculeName: OppBCDF heterotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Oligopeptide transport system permease protein OppB

MacromoleculeName: Oligopeptide transport system permease protein OppB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 33.47307 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLKFILRRCL EAIPTLFILI TISFFMMRLA PGSPFTGERT LPPEVMANIE AKYHLNDPIM TQYFSYLKQL AHGDFGPSFK YKDYSVNDL VASSFPVSAK LGAAAFFLAV ILGVSAGVIA ALKQNTKWDY TVMGLAMTGV VIPSFVVAPL LVMIFAIILH W LPGGGWNG ...String:
MLKFILRRCL EAIPTLFILI TISFFMMRLA PGSPFTGERT LPPEVMANIE AKYHLNDPIM TQYFSYLKQL AHGDFGPSFK YKDYSVNDL VASSFPVSAK LGAAAFFLAV ILGVSAGVIA ALKQNTKWDY TVMGLAMTGV VIPSFVVAPL LVMIFAIILH W LPGGGWNG GALKFMILPM VALSLAYIAS IARITRGSMI EVLHSNFIRT ARAKGLPMRR IILRHALKPA LLPVLSYMGP AF VGIITGS MVIETIYGLP GIGQLFVNGA LNRDYSLVLS LTILVGALTI LFNAIVDVLY AVIDPKIRY

UniProtKB: Oligopeptide transport system permease protein OppB

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Macromolecule #2: Oligopeptide transport system permease protein OppC

MacromoleculeName: Oligopeptide transport system permease protein OppC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 33.046781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMLSKKNSET LENFSEKLEV EGRSLWQDAR RRFMHNRAAV ASLIVLVLIA LFVILAPMLS QFAYDDTDWA MMSSAPDMES GHYFGTDSS GRDLLVRVAI GGRISLMVGV AAALVAVVVG TLYGSLSGYL GGKVDSVMMR LLEILNSFPF MFFVILLVTF F GQNILLIF ...String:
MMLSKKNSET LENFSEKLEV EGRSLWQDAR RRFMHNRAAV ASLIVLVLIA LFVILAPMLS QFAYDDTDWA MMSSAPDMES GHYFGTDSS GRDLLVRVAI GGRISLMVGV AAALVAVVVG TLYGSLSGYL GGKVDSVMMR LLEILNSFPF MFFVILLVTF F GQNILLIF VAIGMVSWLD MARIVRGQTL SLKRKEFIEA AQVGGVSTSG IVIRHIVPNV LGVVVVYASL LVPSMILFES FL SFLGLGT QEPLSSWGAL LSDGANSMEV SPWLLLFPAG FLVVTLFCFN FIGDGLRDAL DPKDR

UniProtKB: Oligopeptide transport system permease protein OppC

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Macromolecule #3: Oligopeptide transport ATP-binding protein OppD

MacromoleculeName: Oligopeptide transport ATP-binding protein OppD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type oligopeptide transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 37.114207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVIETATVP LAQQQADALL NVKDLRVTFS TPDGDVTAVN DLNFSLRAGE TLGIVGESGS GKSQTAFALM GLLAANGRIG GSATFNGRE ILNLPEHELN KLRAEQISMI FQDPMTSLNP YMRVGEQLME VLMLHKNMSK AEAFEESVRM LDAVKMPEAR K RMKMYPHE ...String:
MSVIETATVP LAQQQADALL NVKDLRVTFS TPDGDVTAVN DLNFSLRAGE TLGIVGESGS GKSQTAFALM GLLAANGRIG GSATFNGRE ILNLPEHELN KLRAEQISMI FQDPMTSLNP YMRVGEQLME VLMLHKNMSK AEAFEESVRM LDAVKMPEAR K RMKMYPHE FSGGMRQRVM IAMALLCRPK LLIADEPTTA LDVTVQAQIM TLLNELKREF NTAIIMITHD LVVVAGICDK VL VMYAGRT MEYGNARDVF YQPVHPYSIG LLNAVPRLDA EGETMLTIPG NPPNLLRLPK GCPFQPRCPH AMEICSSAPP LEE FTPGRL RACFKPVEEL

UniProtKB: Oligopeptide transport ATP-binding protein OppD

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Macromolecule #4: Oligopeptide transport ATP-binding protein OppF

MacromoleculeName: Oligopeptide transport ATP-binding protein OppF / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type oligopeptide transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 37.133352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNAVTEGRKV LLEIADLKVH FEIKDGKQWF WQPPKTLKAV DGVTLRLYEG ETLGVVGESG CGKSTFARAI IGLVKATDGH VAWLGKELL GMKPDEWRAV RSDIQMIFQD PLASLNPRMT IGEIIAEPLR TYHPKMSRQE VRERVKAMML KVGLLPNLIN R YPHEFSGG ...String:
MNAVTEGRKV LLEIADLKVH FEIKDGKQWF WQPPKTLKAV DGVTLRLYEG ETLGVVGESG CGKSTFARAI IGLVKATDGH VAWLGKELL GMKPDEWRAV RSDIQMIFQD PLASLNPRMT IGEIIAEPLR TYHPKMSRQE VRERVKAMML KVGLLPNLIN R YPHEFSGG QCQRIGIARA LILEPKLIIC DEPVSALDVS IQAQVVNLLQ QLQREMGLSL IFIAHDLAVV KHISDRVLVM YL GHAVELG TYDEVYHNPL HPYTRALMSA VPIPDPDLEK NKTIQLLEGE LPSPINPPSG CVFRTRCPIA GPECAKTRPV LEG SFRHSV SCLKVDP

UniProtKB: Oligopeptide transport ATP-binding protein OppF

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 367365
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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