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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: PLoS One / Year: 2026
Title: Exploration of a workflow for the classification and identification of co-purified protein complexes yields new structures and multiple MSP assembly states.
Authors: Qingyang Zhang / Abhinandan Venkatesha Murthy / Carsten Mim /
Abstract: Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryo-EM) with its ability to image protein mixtures is the most promising tool ...Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryo-EM) with its ability to image protein mixtures is the most promising tool to enable structural proteomics. Additionally, image processing has evolved and can deal with conformational and compositional heterogeneity. Integrative approaches, namely mass spectrometry in conjunction with cryo-EM, have made it possible to characterize and identify complex mixtures. However, this comes at a cost of generating models and interpreting mass spectra. Here we present a modified approach that builds on publicly available software. By generating maps around 4 Å and unsupervised model building we were able to identify the most abundant proteins in our sample. This sample consisted of co-purified membrane proteins in nanodiscs. We found a novel structure and unexpected nanodisc assemblies. Our maps imply a direct interaction between membrane proteins and membrane scaffolding proteins.
History
DepositionJan 5, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52450_half_map_1.map
Projections & Slices
AxesZYX

Projections

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

Projections

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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