[English] 日本語
Yorodumi
- EMDB-27542: Cryo-EM reveals the molecular basis of laminin polymerization and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27542
TitleCryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies
Map dataUnsharpened map
Sample
  • Complex: Lamimin polymer node
    • Protein or peptide: Laminin subunit alpha-1
    • Protein or peptide: Laminin subunit beta-1
    • Protein or peptide: Laminin subunit gamma-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
KeywordsLaminin / Complex / Basement membrane / STRUCTURAL PROTEIN
Function / homology
Function and homology information


laminin-3 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / retinal blood vessel morphogenesis / L1CAM interactions ...laminin-3 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / retinal blood vessel morphogenesis / L1CAM interactions / regulation of basement membrane organization / morphogenesis of an epithelial sheet / hemidesmosome assembly / positive regulation of integrin-mediated signaling pathway / glycosphingolipid binding / tissue development / Laminin interactions / endoderm development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / branching involved in salivary gland morphogenesis / protein complex involved in cell-matrix adhesion / establishment of epithelial cell apical/basal polarity / camera-type eye development / blood vessel morphogenesis / odontogenesis / extracellular matrix structural constituent / MET activates PTK2 signaling / maintenance of blood-brain barrier / epithelial tube branching involved in lung morphogenesis / positive regulation of muscle cell differentiation / endodermal cell differentiation / regulation of embryonic development / Non-integrin membrane-ECM interactions / basement membrane / positive regulation of cell adhesion / ECM proteoglycans / extracellular matrix disassembly / regulation of cell migration / extracellular matrix / Degradation of the extracellular matrix / substrate adhesion-dependent cell spreading / positive regulation of epithelial cell proliferation / axon guidance / Post-translational protein phosphorylation / animal organ morphogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cell-cell junction / cell migration / retina development in camera-type eye / collagen-containing extracellular matrix / protein-containing complex assembly / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / protein phosphorylation / structural molecule activity / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Laminin IV type B domain / Laminin IV type B / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. ...Laminin IV type B domain / Laminin IV type B / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / 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-type EGF-like (LE) domain profile. / Laminin G domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Laminin subunit beta-1 / Laminin subunit gamma-1 / Laminin subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKulczyk AW
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM reveals the molecular basis oflaminin polymerization and LN-lamininopathies.
Authors: Arkadiusz W Kulczyk / Karen K McKee / Ximo Zhang / Iwona Bizukojc / Ying Q Yu / Peter D Yurchenco /
Abstract: Laminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron ...Laminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron microscopy to determine a 3.7 Å structure of the trimeric laminin polymer node containing α1, β1 and γ1 subunits. The structure reveals the molecular basis of calcium-dependent formation of laminin lattice, and provides insights into polymerization defects manifesting in human disease.
History
DepositionJul 8, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27542.png

Downloads & links

-
Map

FileDownload / File: emd_27542.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Voxel sizeX=Y=Z: 0.972 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.65571874 - 1.0992038
Average (Standard dev.)0.00016770515 (±0.02742768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 291.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpened map

Fileemd_27542_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27542_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_27542_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lamimin polymer node

EntireName: Lamimin polymer node
Components
  • Complex: Lamimin polymer node
    • Protein or peptide: Laminin subunit alpha-1
    • Protein or peptide: Laminin subunit beta-1
    • Protein or peptide: Laminin subunit gamma-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Lamimin polymer node

SupramoleculeName: Lamimin polymer node / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: A trimeric complex of the N-terminal fragments (LN, LE1, LE2 domains) from laminin alpha 1, laminin beta 1 and laminin gamma 1.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 172 KDa

-
Macromolecule #1: Laminin subunit alpha-1

MacromoleculeName: Laminin subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 34.709211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFPAILNLA TNAHISANAT CGEKGPEMFC KLVEHVPGRP VRHAQCRVCD GNSTNPRERH PISHAIDGTN NWWQSPSIQN GREYHWVTV TLDLRQVFQV AYIIIKAANA PRPGNWILER SVDGVKFKPW QYYAVSDTEC LTRYKITPRR GPPTYRADNE V ICTSYYSK ...String:
GLFPAILNLA TNAHISANAT CGEKGPEMFC KLVEHVPGRP VRHAQCRVCD GNSTNPRERH PISHAIDGTN NWWQSPSIQN GREYHWVTV TLDLRQVFQV AYIIIKAANA PRPGNWILER SVDGVKFKPW QYYAVSDTEC LTRYKITPRR GPPTYRADNE V ICTSYYSK LVPLEHGEIH TSLINGRPSA DDPSPQLLEF TSARYIRLRL QRIRTLNADL MTLSHRDLRD LDPIVTRRYY YS IKDISVG GMCICYGHAS SCPWDEEAKQ LQCQCEHNTC GESCDRCCPG YHQQPWRPGT ISSGNECE

UniProtKB: Laminin subunit alpha-1

-
Macromolecule #2: Laminin subunit beta-1

MacromoleculeName: Laminin subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.09191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GCAEGSCYPA TGDLLIGRAQ KLSVTSTCGL HKPEPYCIVS HLQEDKKCFI CNSQDPYHET LNPDSHLIEN VVTTFAPNRL KIWWQSENG VENVTIQLDL EAEFHFTHLI MTFKTFRPAA MLIERSSDFG KTWGVYRYFA YDCEASFPGI STGPMKKVDD I ICDSRYSD ...String:
GCAEGSCYPA TGDLLIGRAQ KLSVTSTCGL HKPEPYCIVS HLQEDKKCFI CNSQDPYHET LNPDSHLIEN VVTTFAPNRL KIWWQSENG VENVTIQLDL EAEFHFTHLI MTFKTFRPAA MLIERSSDFG KTWGVYRYFA YDCEASFPGI STGPMKKVDD I ICDSRYSD IEPSTEGEVI FRALDPAFKI EDPYSPRIQN LLKITNLRIK FVKLHTLGDN LLDSRMEIRE KYYYAVYDMV VR GNCFCYG HASECAPVDG FNEEVEGMVH GHCMCRHNTK GLNCELCMDF YHDLPWRPAE GRNSNACKKC

UniProtKB: Laminin subunit beta-1

-
Macromolecule #3: Laminin subunit gamma-1

MacromoleculeName: Laminin subunit gamma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.110816 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 NDPKVLKSYY YA ISDFAVG GRCKCNGHAS ECMKNEFDKL VCNCKHNTYG VDCEKCLPFF NDRPWRRATA ESASECLP

UniProtKB: Laminin subunit gamma-1

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 125011
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8dmk:
Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies

+
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