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- EMDB-71051: Cryo-EM structure of chicken NEL dimer bound with one human NICOL. -

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Basic information

Entry
Database: EMDB / ID: EMD-71051
TitleCryo-EM structure of chicken NEL dimer bound with one human NICOL.
Map dataCryo-EM structure of chicken NEL dimer bound with one human NICOL.
Sample
  • Complex: 2:1 complex between chicken NEL and human NICOL
    • Protein or peptide: Protein NEL
    • Protein or peptide: NELL2-interacting cell ontogeny regulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsROS1 / NEL / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of retinal ganglion cell axon guidance / transferrin receptor binding / commissural neuron axon guidance / fertilization / neural crest cell migration / 3'-UTR-mediated mRNA stabilization / positive regulation of cell division / positive regulation of neuron differentiation / protein kinase C binding / mRNA 3'-UTR binding ...negative regulation of retinal ganglion cell axon guidance / transferrin receptor binding / commissural neuron axon guidance / fertilization / neural crest cell migration / 3'-UTR-mediated mRNA stabilization / positive regulation of cell division / positive regulation of neuron differentiation / protein kinase C binding / mRNA 3'-UTR binding / heparin binding / spermatogenesis / cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Neuropeptide-like protein / Neuropeptide-like / : / EGF domain / EGF domain / : / Thrombospondin N-terminal -like domains. / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain ...Neuropeptide-like protein / Neuropeptide-like / : / EGF domain / EGF domain / : / Thrombospondin N-terminal -like domains. / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / Laminin G domain / Laminin G domain / von Willebrand factor (vWF) type C domain / VWFC domain / : / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
NELL2-interacting cell ontogeny regulator 1 / Protein NEL
Similarity search - Component
Biological speciesGallus gallus (chicken) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsAn WD / Zhang XW / Bai XC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural Basis for the Activation of the Vertebrate ROS1 Receptor by the NEL/NICOL Ligand Complex
Authors: An WD / Zhang XW / Bai XC
History
DepositionJun 5, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71051.png

Downloads & links

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Map

FileDownload / File: emd_71051.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of chicken NEL dimer bound with one human NICOL.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 260 pix.
= 365.092 Å		1.4 Å/pix.
x 260 pix.
= 365.092 Å		1.4 Å/pix.
x 260 pix.
= 365.092 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4042 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.027739141 - 0.06615349
Average (Standard dev.)-0.000088603294 (±0.0014314771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 365.09198 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of chicken NEL dimer bound with...

Fileemd_71051_half_map_1.map
AnnotationCryo-EM structure of chicken NEL dimer bound with one human NICOL. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of chicken NEL dimer bound with...

Fileemd_71051_half_map_2.map
AnnotationCryo-EM structure of chicken NEL dimer bound with one human NICOL. 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 : 2:1 complex between chicken NEL and human NICOL

EntireName: 2:1 complex between chicken NEL and human NICOL
Components
  • Complex: 2:1 complex between chicken NEL and human NICOL
    • Protein or peptide: Protein NEL
    • Protein or peptide: NELL2-interacting cell ontogeny regulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 2:1 complex between chicken NEL and human NICOL

SupramoleculeName: 2:1 complex between chicken NEL and human NICOL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Protein NEL

MacromoleculeName: Protein NEL / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 91.070969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESGCGLGTL CLLLCLGPVV GFGVDPSLQI DVLSELGLPG YAAGVRQVPG LHNGSKAFLF PDTSRSVKAS PETAEIFFQK LRNKYEFTI LVTLKQAHLN SGVIFSIHHL DHRYLELESS GHRNEIRLHY RTGSHRSHTE VFPYILADDK WHRLSLAISA S HLILHVDC ...String:
MESGCGLGTL CLLLCLGPVV GFGVDPSLQI DVLSELGLPG YAAGVRQVPG LHNGSKAFLF PDTSRSVKAS PETAEIFFQK LRNKYEFTI LVTLKQAHLN SGVIFSIHHL DHRYLELESS GHRNEIRLHY RTGSHRSHTE VFPYILADDK WHRLSLAISA S HLILHVDC NKIYERVVEK PFMDLPVGTT FWLGQRNNAH GYFKGIMQDV QLLVMPQGFI SQCPDLNRTC PTCNDFHGLV QK IMELQDI LAKTSAKLSQ AEQRMNKLDQ CYCERTCTMK GMTYREFESW TDGCKNCTCM NGTVQCEALI CSLSDCPPNS ALS YVDGKC CKECQSVCIF EGRTYFEGQR ETVYSSSGDC VLFECKDHKM QRIPKDSCAT LNCPESQQIP LSHSCCKICK GHDF CTEGH NCMEHSVCRN LDDRAVCSCR DGFRALREDN AYCEDVDECA EGQHYCRENT MCVNTPGSFM CICKTGYIRI DDYSC TEHD ECVTNQHNCD ENALCFNTVG GHNCVCKLGY TGNGTVCKAF CKDGCRNGGA CIASNVCACP QGFTGPSCET DIDECS DGF VQCDSRANCI NLPGWYHCEC RDGYHDNGMF SPSGESCEDI DECATGRHSC ANDTVCFNLD GGYDCRCPHG KNCTGDC IH EDKIKHNGQI WVLENDRCSV CSCQSGYVMC RRMVCDCENP TVDLFCCPEC DPRLSSQCLH QSGELSYNSG DSWIQNCQ Q CRCLQGEVDC WPLPCPEVDC EFSVLPENEC CPRCVTDPCQ ADTIRNDITK TCLDETNVVR FTGSSWIKHG TECTLCQCK NGHVCCSVDP QCLQEL

UniProtKB: Protein NEL

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Macromolecule #2: NELL2-interacting cell ontogeny regulator 1

MacromoleculeName: NELL2-interacting cell ontogeny regulator 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.182 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAPPPACRSP MSPPPPPLLL LLLSLALLGA RARAEPAGSA VPAQSRPCVD CHAFEFMQRA LQDLRKTACS LDARTETLLL QAERRALCA CWPAGH

UniProtKB: NELL2-interacting cell ontogeny regulator 1

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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: 7 / 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

Concentration8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Made in RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 33485
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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