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- EMDB-71685: Cryo-EM structure of human NXPE1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71685
TitleCryo-EM structure of human NXPE1
Map datafinal map
Sample
  • Complex: dimer of NXPE1
    • Protein or peptide: NXPE family member 1
  • Ligand: ACETYL COENZYME *A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordssialic acid / acetyltransferase / HYDROLASE
Function / homology: / NXPE family member 4-like, C-terminal domain / Neurexophilin/NXPE / Neurexophilin / Immunoglobulin E-set / Immunoglobulin-like fold / extracellular region / NXPE family member 1
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang H / Li F / Piper D / Min X
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biorxiv / Year: 2026
Title: Structure and function of human NXPE1, a sialic acid O-acetyltransferase
Authors: Zhang H / Li F / Zhang M / Konno H / Yu W / Min X / Paulchakrabarti M / Choudhury B / Simons A / Piper D / Hsu H / Ouyang W
History
DepositionJul 12, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71685.png

Downloads & links

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Map

FileDownload / File: emd_71685.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 325.2 Å		0.81 Å/pix.
x 400 pix.
= 325.2 Å		0.81 Å/pix.
x 400 pix.
= 325.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.813 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.8760281 - 1.5987431
Average (Standard dev.)0.0000045762813 (±0.025418114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 325.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_71685_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_71685_half_map_2.map
Annotationhalf 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 : dimer of NXPE1

EntireName: dimer of NXPE1
Components
  • Complex: dimer of NXPE1
    • Protein or peptide: NXPE family member 1
  • Ligand: ACETYL COENZYME *A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: dimer of NXPE1

SupramoleculeName: dimer of NXPE1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: NXPE family member 1

MacromoleculeName: NXPE family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.261863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNL SISVHYWNNS AKSLFPKTSL IPLKPLTETE LRIKEIIEKL DQQIPPRPF THVNTTTSAT HSTATILNPR DTYCRGDQLD ILLEVRDHLG QRKQYGGDFL RARMSSPALT AGASGKVMDF N NGTYLVSF ...String:
MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNL SISVHYWNNS AKSLFPKTSL IPLKPLTETE LRIKEIIEKL DQQIPPRPF THVNTTTSAT HSTATILNPR DTYCRGDQLD ILLEVRDHLG QRKQYGGDFL RARMSSPALT AGASGKVMDF N NGTYLVSF TLFWEGQVSL SLLLIHPSEG ASALWRARNQ GYDKIIFKGK FVNGTSHVFT ECGLTLNSNA ELCEYLDDRD QE AFYCMKP QHMPCEALTY MTTRNREVSY LTDKENSLFH RSKVGVEMMK DRKHIDVTNC NKREKIEETC QVGMKPPVPG GYT LQGKWI TTFCNQVQLD TIKINGCLKG KLIYLLGDST LRQWIYYFPK VVKTLKFFDL HETGIFKKHL LLDAERHTQI QWKK HSYPF VTFQLYSLID HDYIPREIDR LSGDKNTAIV ITFGQHFRPF PIDIFIRRAI GVQKAIERLF LRSPATKVII KTENI REMH IETERFGDFH GYIHYLIMKD IFKDLNVGII DAWDMTIAYG TDTIHPPDHV IGNQINMFLN YIC

UniProtKB: NXPE family member 1

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Macromolecule #3: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 3 / Number of copies: 2 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 106947
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 114.9
Output model

PDB-9pja:
Cryo-EM structure of human NXPE1

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