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- EMDB-27542: Cryo-EM reveals the molecular basis of laminin polymerization and... -

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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 ION
KeywordsLaminin / Complex / Basement membrane / STRUCTURAL PROTEIN
Function / homology
Function and homology information


laminin-3 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-11 complex / laminin complex / laminin-2 complex / laminin-8 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions ...laminin-3 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-11 complex / laminin complex / laminin-2 complex / laminin-8 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions / retinal blood vessel morphogenesis / morphogenesis of an epithelial sheet / hemidesmosome assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / 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 / branching involved in salivary gland morphogenesis / endoderm development / establishment of epithelial cell apical/basal polarity / odontogenesis / extracellular matrix structural constituent / MET activates PTK2 signaling / positive regulation of muscle cell differentiation / epithelial tube branching involved in lung morphogenesis / maintenance of blood-brain barrier / endodermal cell differentiation / regulation of embryonic development / basement membrane / Non-integrin membrane-ECM interactions / extracellular matrix disassembly / ECM proteoglycans / Degradation of the extracellular matrix / extracellular matrix / positive regulation of cell adhesion / substrate adhesion-dependent cell spreading / regulation of cell migration / 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) / neuron projection development / cell-cell junction / cell migration / retina development in camera-type eye / protein-containing complex assembly / : / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / protein phosphorylation / endoplasmic reticulum lumen / signaling receptor binding / perinuclear region of cytoplasm / structural molecule activity / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / 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) ...LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / 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 G 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 / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / EGF-like domain signature 1. / EGF-like domain signature 2. / 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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27542.png

Downloads & links

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Map

FileDownload / File: emd_27542.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 300 pix.
= 291.6 Å		0.97 Å/pix.
x 300 pix.
= 291.6 Å		0.97 Å/pix.
x 300 pix.
= 291.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.972 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_27542_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27542_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27542_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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 ION

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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

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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

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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

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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

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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: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: CALCIUM ION

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

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.8 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

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Image processing

Startup modelType of model: NONE
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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