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- EMDB-52450: Structure of Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabino... -

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Basic information

Entry
Database: EMDB / ID: EMD-52450
TitleStructure of Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase embedded in nanodisc
Map dataUnsharpened Map
Sample
  • Complex: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
    • Protein or peptide: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
KeywordsTransferase / MEMBRANE PROTEIN
Function / homology
Function and homology information


undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase activity / 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / : / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsMim C / Zhang Q / Murthy AV
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 21:1630 Sweden
CitationJournal: To Be Published
Title: In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states
Authors: Zhang Q / Murthy AV / Mim C
History
DepositionJan 5, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52450.png

Downloads & links

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Map

FileDownload / File: emd_52450.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened Map
Voxel sizeX=Y=Z: 0.66 Å
Density
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.36020404 - 0.45936784
Average (Standard dev.)-0.0014911935 (±0.021537367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52450_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map sharpened with DeepMhancer

Fileemd_52450_additional_1.map
AnnotationMap sharpened with DeepMhancer
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52450_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52450_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric complex of ACRB transporter co-purified from E.coli in n...

EntireName: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
Components
  • Complex: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
    • Protein or peptide: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

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Supramolecule #1: Trimeric complex of ACRB transporter co-purified from E.coli in n...

SupramoleculeName: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

MacromoleculeName: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.382086 KDa
SequenceString: MFEIHPVKKV SVVIPVYNEQ ESLPELIRRT TTACESLGKE YEILLIDDGS SDNSAHMLVE ASQAENSHIV SILLNRNYGQ HSAIMAGFS HVTGDLIITL DADLQNPPEE IPRLVAKADE GYDVVGTVRQ NRQDSWFRKT ASKMINRLIQ RTTGKAMGDY G CMLRAYRR ...String:
MFEIHPVKKV SVVIPVYNEQ ESLPELIRRT TTACESLGKE YEILLIDDGS SDNSAHMLVE ASQAENSHIV SILLNRNYGQ HSAIMAGFS HVTGDLIITL DADLQNPPEE IPRLVAKADE GYDVVGTVRQ NRQDSWFRKT ASKMINRLIQ RTTGKAMGDY G CMLRAYRR HIVDAMLHCH ERSTFIPILA NIFARRAIEI PVHHAEREFG ESKYSFMRLI NLMYDLVTCL TTTPLRMLSL LG SIIAIGG FSIAVLLVIL RLTFGPQWAA EGVFMLFAVL FTFIGAQFIG MGLLGEYIGR IYTDVRARPR YFVQQVIRPS SKE NE

UniProtKB: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

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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

Concentration4.6 mg/mL
BufferpH: 7.5 / Details: 50mM HEPES, 150mM NaCl and 5mM EGTA
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: 100% humidity, 16C.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 544237
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 48142
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

2hrt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: BACKBONE TRACE
Output model

PDB-9hwj:
Structure of Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase embedded in nanodisc

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