[English] 日本語
Yorodumi
- EMDB-44008: Cryo-EM reveals molecular mechanisms underlying the inhibitory ef... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44008
TitleCryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation
Map dataCryo-EM structure of Net4dC_LmG1: sharpened map
Sample
  • Complex: Net4dC-LmG1dC
    • Protein or peptide: Laminin subunit gamma-1
    • Protein or peptide: Netrin-4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNetrin-4 / Laminin G1 / Complex / Basement membrane / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling / Netrin-1 signaling / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions / hemidesmosome assembly / laminin-1 binding / positive regulation of integrin-mediated signaling pathway ...regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling / Netrin-1 signaling / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions / hemidesmosome assembly / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Laminin interactions / Formation of the dystrophin-glycoprotein complex (DGC) / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / endoderm development / extracellular matrix structural constituent / MET activates PTK2 signaling / neuron remodeling / positive regulation of muscle cell differentiation / maintenance of blood-brain barrier / basement membrane / Non-integrin membrane-ECM interactions / extracellular matrix disassembly / ECM proteoglycans / Degradation of the extracellular matrix / substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / positive regulation of epithelial cell proliferation / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell migration / : / protein-containing complex assembly / cell adhesion / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Netrin-4, NTR domain / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) ...Netrin-4, NTR domain / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / : / Laminin/attractin EGF domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Epidermal growth factor-like domain. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Laminin subunit gamma-1 / Netrin-4
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKulczyk AW
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation.
Authors: Arkadiusz W Kulczyk / Karen K McKee / Peter D Yurchenco /
Abstract: Netrin-4 is a tumor suppressor that interferes with formation of the laminin lattice. We employed cryo-electron microscopy to determine a structure of the protein complex consisting of the N-terminal ...Netrin-4 is a tumor suppressor that interferes with formation of the laminin lattice. We employed cryo-electron microscopy to determine a structure of the protein complex consisting of the N-terminal fragments from netrin-4 and laminin γ1. The structure reveals that netrin-4 binds laminin γ1 at the molecular interface where laminin β1 would have bound, thus inhibiting the assembly of the heterotrimeric laminin polymer nodes consisting of α1, β1, and γ1 subunits, and their polymerization into the extracellular lattice. The four orders of magnitude higher affinity of the netrin-4-laminin γ1 interaction results from the larger buried surface area than the one formed by β1 and γ1 laminins and greater electrostatic surface complementarity. Our findings, supported by site-directed mutagenesis, solid-phase binding analysis, laminin polymerization, and Schwann cell assays, collectively demonstrate that, in addition to inhibiting laminin polymerization, netrin-4 disassembles the pre-existing laminin lattice. The structure has the potential to facilitate the development of novel therapies for cancer treatment.
History
DepositionMar 9, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44008.png

Downloads & links

-
Map

FileDownload / File: emd_44008.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Net4dC_LmG1: sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 192 pix.
= 248.832 Å		1.3 Å/pix.
x 192 pix.
= 248.832 Å		1.3 Å/pix.
x 192 pix.
= 248.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.008
Minimum - Maximum-0.02592705 - 0.11453716
Average (Standard dev.)0.000086775595 (±0.0015274837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 248.832 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_44008_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of Net4dC LmG1: sharpened map

Fileemd_44008_half_map_1.map
AnnotationCryo-EM structure of Net4dC_LmG1: sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of Net4dC LmG1: sharpened map

Fileemd_44008_half_map_2.map
AnnotationCryo-EM structure of Net4dC_LmG1: sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Net4dC-LmG1dC

EntireName: Net4dC-LmG1dC
Components
  • Complex: Net4dC-LmG1dC
    • Protein or peptide: Laminin subunit gamma-1
    • Protein or peptide: Netrin-4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Net4dC-LmG1dC

SupramoleculeName: Net4dC-LmG1dC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: A dimeric complex of the N-terminal fragments from netrin-4 and laminin gamma 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61 KDa

-
Macromolecule #1: Laminin subunit gamma-1

MacromoleculeName: Laminin subunit gamma-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.152922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDECTDEGGR PQRCMPEFVN AAFNVTVVAT NTCGTPPEEY CVQTGVTGVT KSCHLCDAGQ PHLQHGAAFL TDYNNQADTT WWQSQTMLA GVQYPSSINL TLHLGKAFDI TYVRLKFHTS RPESFAIYKR TWEDGPWIPY QYYSGSCENT YSKANRGFIR T GGDEQQAL ...String:
MDECTDEGGR PQRCMPEFVN AAFNVTVVAT NTCGTPPEEY CVQTGVTGVT KSCHLCDAGQ PHLQHGAAFL TDYNNQADTT WWQSQTMLA GVQYPSSINL TLHLGKAFDI TYVRLKFHTS RPESFAIYKR TWEDGPWIPY QYYSGSCENT YSKANRGFIR T GGDEQQAL CTDEFSDISP LTGGNVAFST LEGRPSAYNF DNSPVLQEWV TATDISVTLN RLNTFGDEVF NRPKVLKSYY YA ISDFAVG GRCKCNGHAS ECMKNEFDKL VCNCKHNTYG VDCEKCLPFF NDRPWRRATA ESASECLP

UniProtKB: Laminin subunit gamma-1

-
Macromolecule #2: Netrin-4

MacromoleculeName: Netrin-4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 32.177734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LGRKLRADTM CGQNATELFC FYSENADLTC RQPKCDKCNA AHSHLAHPPS AMADSSFRFP RTWWQSAEDV HREKIQLDLE AEFYFTHLI MVFKSPRPAA MVLDRSQDFG KTWKPYKYFA TNCSATFGLE DDVVKKGAIC TSRYSNPFPC TGGEVIFRAL S PPYDIENP ...String:
LGRKLRADTM CGQNATELFC FYSENADLTC RQPKCDKCNA AHSHLAHPPS AMADSSFRFP RTWWQSAEDV HREKIQLDLE AEFYFTHLI MVFKSPRPAA MVLDRSQDFG KTWKPYKYFA TNCSATFGLE DDVVKKGAIC TSRYSNPFPC TGGEVIFRAL S PPYDIENP YSAKVQEQLK ITNLRVRLLK RQSCPCQIND LNAKPHHFMH YAVYDFIVKG SCFCNGHADQ CLPVEGFRPI KA PGAFHVV HGRCMCKHNT AGSHCQHCAP LYNDRPWEAA DGRTGAP

UniProtKB: Netrin-4

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 7 / 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

BufferpH: 7.5
GridModel: Quantifoil / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9az3:
Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation

+
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