[English] 日本語
Yorodumi
- EMDB-71058: Cryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71058
TitleCryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2.
Map dataCryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2.
Sample
  • Complex: 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL
    • Protein or peptide: Protein NEL
    • Protein or peptide: NELL2-interacting cell ontogeny regulator 1
    • Protein or peptide: Tyrosine-protein kinase receptor
  • 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 / columnar/cuboidal epithelial cell development / regulation of phosphate transport / transferrin receptor binding / regulation of TOR signaling / commissural neuron axon guidance / fertilization / neural crest cell migration / 3'-UTR-mediated mRNA stabilization / positive regulation of cell division ...negative regulation of retinal ganglion cell axon guidance / columnar/cuboidal epithelial cell development / regulation of phosphate transport / transferrin receptor binding / regulation of TOR signaling / commissural neuron axon guidance / fertilization / neural crest cell migration / 3'-UTR-mediated mRNA stabilization / positive regulation of cell division / regulation of ERK1 and ERK2 cascade / transmembrane receptor protein tyrosine kinase activity / positive regulation of neuron differentiation / cell surface receptor protein tyrosine kinase signaling pathway / protein kinase C binding / mRNA 3'-UTR binding / receptor protein-tyrosine kinase / heparin binding / gene expression / protein phosphatase binding / spermatogenesis / cell population proliferation / receptor complex / negative regulation of gene expression / calcium ion binding / perinuclear region of cytoplasm / cell surface / extracellular space / ATP binding / identical protein binding / plasma membrane / 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 / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Six-bladed beta-propeller, TolB-like / 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. / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein kinase receptor / NELL2-interacting cell ontogeny regulator 1 / Protein NEL
Similarity search - Component
Biological speciesGallus gallus (chicken) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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

-
Structure visualization

Supplemental images

emd_71058.png

Downloads & links

-
Map

FileDownload / File: emd_71058.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 400 pix.
= 561.68 Å		1.4 Å/pix.
x 400 pix.
= 561.68 Å		1.4 Å/pix.
x 400 pix.
= 561.68 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-0.029463714 - 0.0643804
Average (Standard dev.)0.000014610374 (±0.0011526856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 561.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Cryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2....

Fileemd_71058_half_map_1.map
AnnotationCryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2....

Fileemd_71058_half_map_2.map
AnnotationCryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2. Half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL

EntireName: 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL
Components
  • Complex: 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL
    • Protein or peptide: Protein NEL
    • Protein or peptide: NELL2-interacting cell ontogeny regulator 1
    • Protein or peptide: Tyrosine-protein kinase receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL

SupramoleculeName: 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gallus gallus (chicken)

-
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

-
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

-
Macromolecule #3: Tyrosine-protein kinase receptor

MacromoleculeName: Tyrosine-protein kinase receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 261.174797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRNACLLLNR LGAFYFIWIS AAYCSFSKNC QDLCTSNLEG ELGIANLCNV SDINVACTQG CQFWNATEQV NCPLKCNKTY TRECETVSC KFGCSRAEDA YGVEAQNCLN KPGAPFASSI GSHNITLGWK PANISEVKYI IQWKFHQLPG DWRYTEVVSE T SYTVKDLQ ...String:
MRNACLLLNR LGAFYFIWIS AAYCSFSKNC QDLCTSNLEG ELGIANLCNV SDINVACTQG CQFWNATEQV NCPLKCNKTY TRECETVSC KFGCSRAEDA YGVEAQNCLN KPGAPFASSI GSHNITLGWK PANISEVKYI IQWKFHQLPG DWRYTEVVSE T SYTVKDLQ AFTEYEFRVV WIITSQLQLH SPPSPSYRTH ASGVPTTAPI IKDIQSSSPN TVEVSWFPPL FPNGLIVGYN LV LTSENHE LLRASRGHSF QFYSTFPNST YRFSIVAVNE AGAGPPAEAN ITTPESKVKE KAKWLFLSRN QSLRKRYMEH FLE AAHCLQ NGIIHHNITG ISVNVYQQVV YFSEGNSIWV KGVVDMSDVS DLTLFYTGWG NITSISVDWL YQRMYFVMNE KIHV CQLEN CTAAEDITPP YVTSPRKIVA DPYNGYIFCL LEDGIYRANL PLFPDTASAA SLVVKSHTLR DFMINFQSKR LIFFN KTEQ AFVSGFLDGS EFHTLRAHVP LDDMESFVYE DNIFTVTDGR AVFHEEISQV GSSSFNEYVV DCSLEYPEYF GFGNLL FYA ASTQPYPLPT LPRLVTVLFG SDQAVISWSP PEYTIGTSRS AWQNWTYDVK VSSQSTFEEE WVVSNITDTR FAVKNLV SF TEYEMSVRAV SPAGEGPWSE PFRGMTFEEA EEEPYILAVG AEGLWKQRLD SYGPGEFLYP HIRNISDLDW YNDTLYWS N SMGKVQTWSM NKKEGTTENS YVPDIKNARM LAFDWLGQCL YWAGKANTIY RKSLLGDHMD VVAHVVYVVK DLAVDSVNG YLYWATTYTV ESARLNGEEY LILQEHLQFS GKQVVGLALD LTSGFLYWLV QDGLCLNLYR ISICKESCGN IMVTEISAWS VSEVSQNAL QYYSGRLFWI NRLKFITTQE LNQSISIPFS EPAEFAAFTL VHTSLKPLPG NFSFTPKVIP SSVPESSFKI K GNSSSFHI IWNASTDVQW GTVFYCVGSN ALQMRTLESE RCLHPHDLTV PSYKVDWLEP FTLFDFSVTP YTYWGKAPTT SV YLRAPEG VPSAPANPRI YVLHSNTHEG EEKVLVELRW DKPERDNGVL TQFRVYYQLL YESGAADTLM EWNVSDVKPT ALL FSIRDV HPRLTVRFQV QAFTSVGPGP MSDVAQRNSS DIFPVPTLIT FSSNKLFLTD IDSNHTIWEV LTNRNIKDIC YTAD DDKVY YILEDSLFLL NVQSTSESQL FEDVFLRNVT AITVDWIARH LFVAMKTSWN ETQVFFIDLE LKTKSLKALN IQLGK RNST ISSLLSYPFL SRLYWIEELD YGSRMFYYDI LNNTMYHILG YESVEEKMRN YCNCNVAEAE LGRPISIDVT DIKKPQ LLF IRGRDEIWAS DVDGCHCWRI TKIPSFQGTK IGSLTVDKQF IYWTIEKKEY TEICLADKES TRHSLQRKAN HELKILA YS SAMQSYPDKK CLTPLLDTEK PTILDTTNTS FTLSLPSVTT QQLCPSISQP TPTYLVFFRE ITSNHENSTY HFSTLLQK T LEIQEPIAVI NNLKPFSSYA IQVAVKNYYS NQNQLAVGRE TISTTLYGVP EGVDSIKTVV LSDTTINISW SEPLEPNGP LESIRYQISV NLLSLFPEAP LRKSEFPNGT LSWSVSDLQS GTNNLFKVLA FHPNENWFSE SVPVIAKTFE TPLSPSNIIP RNTSFQLEW RAPLHINGTS FWFELRKWQT RSDWFSPAST TCTVGPVYTC NLTGTLPSAN YLVRATVVYV TGMKSTSSPT S FKTTAGVP SKPGTPKRAE DSKNSVQWEK AEDNGSNLTY YILESRKQSG NTNKVKSLWV VVYNGSCDSI CTWKAENLEG TF QFRAAAA NMLGLGEYSD TSKDIVLAKD TVTSPDITAI VAVIGAVVLG LTIIILFGFV WHQRWKSRKP ASTGQIVLVK EDK ELAQLR GMAETVGLAN ACYAVSTLPS QAEIESLPAF PRDKLNLHKL LGSGAFGEVY EGTALDILAD GSGESRVAVK TLKR GATDQ EKSEFLKEAH LMSKFDHPHI LKLLGVCLLN EPQYLILELM EGGDLLSYLR GARKQKFQSP LLTLTDLLDI CLDIC KGCV YLEKMRFIHR DLAARNCLVS EKQYGSCSRV VKIGDFGLAR DIYKNDYYRK RGEGLLPVRW MAPESLIDGV FTNHSD VWA FGVLVWETLT LGQQPYPGLS NIEVLHHVRS GGRLESPNNC PDDIRDLMTR CWAQDPHNRP TFFYIQHKLQ EIRHSPL CF SYFLGDKESV AGFINQAFED IDVPPADSDS ILSTTLMEAR DQEGLNYLVV VKESNQDQGS ISSAELTSV

UniProtKB: Tyrosine-protein kinase receptor

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 28 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Made in RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 16841
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more