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- EMDB-72623: Extracellular domain of human FAM171A2 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72623
TitleExtracellular domain of human FAM171A2
Map dataExtracellular domain of human FAM171A2
Sample
  • Complex: trimeric human FAM171A2 extracellular domain
    • Protein or peptide: Protein FAM171A2
Keywordstrimeric / neuronal receptor / extracellular / MEMBRANE PROTEIN
Function / homologyFAM171 / : / : / FAM171A1/A2/B, N-terminal / FAM171A1/A2/B C-terminal / membrane / Protein FAM171A2
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsBird TW / Comoletti D / Hanssen E / Valimehr S
Funding support New Zealand, 1 items
OrganizationGrant numberCountry
Other private New Zealand
CitationJournal: Biorxiv / Year: 2026
Title: The trimeric structures of the extracellular domains of FAM171A1 and FAM171A2 neuronal proteins belong to a novel structural superfamily
Authors: Bird T / Valimehr S / Wood DM / Tillett ZD / Kresik L / Mittelstadt G / De Pol F / Meijer DH / Dobson RC / de Wit J / Hanssen E / Comoletti D
History
DepositionSep 8, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72623.png

Downloads & links

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Map

FileReleased
AnnotationExtracellular domain of human FAM171A2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 192 pix.
= 159.936 Å		0.83 Å/pix.
x 192 pix.
= 159.936 Å		0.83 Å/pix.
x 192 pix.
= 159.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.053397905 - 0.16391183
Average (Standard dev.)0.0013476051 (±0.0071613607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 159.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_72623_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72623_half_map_2.map
AnnotationHalf Map A
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 human FAM171A2 extracellular domain

EntireName: trimeric human FAM171A2 extracellular domain
Components
  • Complex: trimeric human FAM171A2 extracellular domain
    • Protein or peptide: Protein FAM171A2

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Supramolecule #1: trimeric human FAM171A2 extracellular domain

SupramoleculeName: trimeric human FAM171A2 extracellular domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein FAM171A2

MacromoleculeName: Protein FAM171A2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.521916 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LEVLFQGPSP QEILIKVQVY VSGELVPLAR ASVDVFGNRT LLAAGTTDSE GVATLPLSYR LGTWVLVTAA RPGFLTNSVP WRVDKLPLY ASVSLYLLPE RPATLILYED LVHILLGSPG ARSQPLVQFQ RRAARLPVSS TYSQLWASLT PASTQQEMRA F PAFLGTEA ...String:
LEVLFQGPSP QEILIKVQVY VSGELVPLAR ASVDVFGNRT LLAAGTTDSE GVATLPLSYR LGTWVLVTAA RPGFLTNSVP WRVDKLPLY ASVSLYLLPE RPATLILYED LVHILLGSPG ARSQPLVQFQ RRAARLPVSS TYSQLWASLT PASTQQEMRA F PAFLGTEA SSSGNGSWLE LIPLAAVSVH LLTGNGTEVP LSGPIHLSLP VPSEPRALAV GTSIPAWRFD PKSGLWVRNG TG VIRKEGR QLYWTFVSPQ LGYWVAAMAL EVLFQ

UniProtKB: Protein FAM171A2

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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: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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: 1.2 µm / Nominal defocus min: 0.6 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2140563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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