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- EMDB-51292: Structure of E. coli YbbAP with bound ATP analogue -

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Basic information

Entry
Database: EMDB / ID: EMD-51292
TitleStructure of E. coli YbbAP with bound ATP analogue
Map dataYbbAP with bound ATP analogue Full map
Sample
  • Complex: YbbAP with bound ATP analogue
    • Protein or peptide: Uncharacterized ABC transporter permease YbbP
    • Protein or peptide: Uncharacterized ABC transporter ATP-binding protein YbbA
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsType VII ABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Membrane component of ABC transporter, predicted / : / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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. ...Membrane component of ABC transporter, predicted / : / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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
Uncharacterized ABC transporter ATP-binding protein YbbA / Uncharacterized ABC transporter permease YbbP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsMcAndrew MBL / Crow A
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N014294/1 United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Structure of YbbAP-TesA: a Type VII ABC transporter lipid-hydrolase complex
Authors: McAndrew MB / Cook J / Gill A / Sahoo K / Thomas C / Stansfeld PJ / Crow A
History
DepositionAug 7, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51292.png

Downloads & links

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Map

FileDownload / File: emd_51292.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYbbAP with bound ATP analogue Full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 252 pix.
= 210.42 Å		0.84 Å/pix.
x 252 pix.
= 210.42 Å		0.84 Å/pix.
x 252 pix.
= 210.42 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.006616012 - 0.021656485
Average (Standard dev.)0.000083074876 (±0.00096621603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 210.42 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map from PHENIX

Fileemd_51292_additional_1.map
AnnotationSharpened map from PHENIX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: YbbAP with bound ATP analogue Half map 1

Fileemd_51292_half_map_1.map
AnnotationYbbAP with bound ATP analogue Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: YbbAP with bound ATP analogue Half map 2

Fileemd_51292_half_map_2.map
AnnotationYbbAP with bound ATP analogue Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YbbAP with bound ATP analogue

EntireName: YbbAP with bound ATP analogue
Components
  • Complex: YbbAP with bound ATP analogue
    • Protein or peptide: Uncharacterized ABC transporter permease YbbP
    • Protein or peptide: Uncharacterized ABC transporter ATP-binding protein YbbA
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: YbbAP with bound ATP analogue

SupramoleculeName: YbbAP with bound ATP analogue / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 138.362 KDa

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Macromolecule #1: Uncharacterized ABC transporter permease YbbP

MacromoleculeName: Uncharacterized ABC transporter permease YbbP / type: protein_or_peptide / ID: 1
Details: Type VII ABC Transporter Transmembrane Protein YbbP
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 89.413836 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIARWFWREW RSPSLLIVWL ALSLAVACVL ALGNISDRME KGLSQQSREF MAGDRALRSS REVPQAWLEE AQKRGLKVGK QLTFATMTF AGDTPQLANV KAVDDIYPMY GDLQTNPPGL KPQAGSVLLA PRLMALLNLK TGDTIDVGDA TLRIAGEVIQ E PDSGFNPF ...String:
MIARWFWREW RSPSLLIVWL ALSLAVACVL ALGNISDRME KGLSQQSREF MAGDRALRSS REVPQAWLEE AQKRGLKVGK QLTFATMTF AGDTPQLANV KAVDDIYPMY GDLQTNPPGL KPQAGSVLLA PRLMALLNLK TGDTIDVGDA TLRIAGEVIQ E PDSGFNPF QMAPRLMMNL ADVDKTGAVQ PGSRVTWRYK FGGNENQLDG YEKWLLPQLK PEQRWYGLEQ DEGALGRSME RS QQFLLLS ALLTLLLAVA AVAVAMNHYC RSRYDLVAIL KTLGAGRAQL RKLIVGQWLM VLTLSAVTGG AIGLLFENVL MVL LKPVLP AALPPASLWP WLWALGTMTV ISLLVGLRPY RLLLATQPLR VLRNDVVANV WPLKFYLPIV SVVVVLLLAG LMGG SMLLW AVLAGAVVLA LLCGVLGWML LNVLRRMTLK SLPLRLAVSR LLRQPWSTLS QLSAFSLSFM LLALLLVLRG DLLDR WQQQ LPPESPNYFL INIATEQVAP LKAFLAEHQI VPESFYPVVR ARLTAINDKP TEGNEDEALN RELNLTWQNT RPDHNP IVA GNWPPKADEV SMEEGLAKRL NVALGDTVTF MGDTQEFRAK VTSLRKVDWE SLRPNFYFIF PEGALDGQPQ SWLTSFR WE NGNGMLTQLN RQFPTISLLD IGAILKQVGQ VLEQVSRALE VMVVLVTACG MLLLLAQVQV GMRQRHQELV VWRTLGAG K KLLRTTLWCE FAMLGFVSGL VAAIGAETAL AVLQAKVFDF PWEPDWRLWI VLPCSGALLL SLFGGWLGAR LVKGKALFR QFAG

UniProtKB: Uncharacterized ABC transporter permease YbbP

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Macromolecule #2: Uncharacterized ABC transporter ATP-binding protein YbbA

MacromoleculeName: Uncharacterized ABC transporter ATP-binding protein YbbA
type: protein_or_peptide / ID: 2 / Details: Type VII ABC Transporter ATP-Binding Protein YbbA / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 26.182629 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPMPAENI VEVHHLKKSV GQGEHELSIL TGVELVVKRG ETIALVGESG SGKSTLLAIL AGLDDGSSGE VSLVGQPLH NMDEEARAKL RAKHVGFVFQ SFMLIPTLNA LENVELPALL RGESSAESRN GAKALLEQLG LGKRLDHLPA Q LSGGEQQR ...String:
MGSSHHHHHH SQDPMPAENI VEVHHLKKSV GQGEHELSIL TGVELVVKRG ETIALVGESG SGKSTLLAIL AGLDDGSSGE VSLVGQPLH NMDEEARAKL RAKHVGFVFQ SFMLIPTLNA LENVELPALL RGESSAESRN GAKALLEQLG LGKRLDHLPA Q LSGGEQQR VALARAFNGR PDVLFADEPT GNLDRQTGDK IADLLFSLNR EHGTTLIMVT HDLQLAARCD RCLRLVNGQL QE EA

UniProtKB: Uncharacterized ABC transporter ATP-binding protein YbbA

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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

BufferpH: 7.2
Component:
ConcentrationName
150.0 mMsodium chloride
20.0 mMHEPES
0.005 %LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 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) / Number grids imaged: 1 / Number real images: 4093 / Average exposure time: 2.2 sec. / Average electron dose: 50.80139123 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 677670
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Software - details: beta
Details: Map resolution of 3.66A reported by Phenix using masked FSC (half map 1,2) = 0.143. Mask smoothing radius is 7.30 A.
Number images used: 52834
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9ge7:
Structure of E. coli YbbAP with bound ATP analogue

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