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- EMDB-67698: Laminin 511 in complex with BCAM -

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Basic information

Entry
Database: EMDB / ID: EMD-67698
TitleLaminin 511 in complex with BCAM
Map data
Sample
  • Complex: Laminin 511 in complex with BCAM
    • Protein or peptide: Basal cell adhesion molecule
    • Protein or peptide: Laminin subunit alpha-5
    • Protein or peptide: Laminin subunit beta-1
    • Protein or peptide: Laminin subunit gamma-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLaminin 511 / BCAM / CELL ADHESION
Function / homology
Function and homology information


laminin-332 trimer / laminin-522 trimer / laminin-523 trimer / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-321 trimer / laminin-421 trimer / extracellular matrix of synaptic cleft / laminin-311 trimer / laminin-411 trimer / laminin-521 trimer ...laminin-332 trimer / laminin-522 trimer / laminin-523 trimer / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-321 trimer / laminin-421 trimer / extracellular matrix of synaptic cleft / laminin-311 trimer / laminin-411 trimer / laminin-521 trimer / laminin-111 trimer / laminin-121 trimer / laminin-511 trimer / laminin-213 trimer / laminin-221 trimer / laminin-211 trimer / regulation of basement membrane organization / L1CAM interactions / hemidesmosome assembly / positive regulation of skeletal muscle acetylcholine-gated channel clustering / endoderm development / protein complex involved in cell-matrix adhesion / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / postsynapse organization / Attachment of bacteria to epithelial cells / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of cell adhesion / Formation of the dystrophin-glycoprotein complex (DGC) / skeletal system morphogenesis / odontogenesis / MET activates PTK2 signaling / positive regulation of muscle cell differentiation / endodermal cell differentiation / maintenance of blood-brain barrier / extracellular matrix structural constituent / basement membrane / laminin receptor activity / extracellular matrix disassembly / Non-integrin membrane-ECM interactions / regulation of cell adhesion / ECM proteoglycans / substrate adhesion-dependent cell spreading / cell-matrix adhesion / Degradation of the extracellular matrix / positive regulation of epithelial cell proliferation / regulation of cell migration / laminin binding / positive regulation of cell adhesion / synaptic cleft / integrin-mediated signaling pathway / regulation of embryonic development / Developmental Lineage of Pancreatic Ductal Cells / Post-translational protein phosphorylation / neuromuscular junction / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / angiogenesis / transmembrane signaling receptor activity / cell migration / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / cell adhesion / extracellular matrix / : / positive regulation of cell migration / receptor ligand activity / endoplasmic reticulum lumen / external side of plasma membrane / glutamatergic synapse / perinuclear region of cytoplasm / structural molecule activity / signal transduction / enzyme binding / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Laminin domain II / : / : / 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 I / Laminin IV ...Laminin domain II / : / : / 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 I / 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 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. / TNFR/NGFR cysteine-rich region / Laminin G domain / Laminin G domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Epidermal growth factor-like domain. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Laminin subunit alpha-5 / Laminin subunit beta-1 / Laminin subunit gamma-1 / Basal cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhou C / Zheng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Laminin 511 in complex with BCAM
Authors: Zhou C / Zheng Y
History
DepositionDec 14, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67698.png

Downloads & links

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Map

FileDownload / File: emd_67698.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-2.0535119 - 2.5088778
Average (Standard dev.)-0.000011565388 (±0.040188055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67698_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_67698_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 : Laminin 511 in complex with BCAM

EntireName: Laminin 511 in complex with BCAM
Components
  • Complex: Laminin 511 in complex with BCAM
    • Protein or peptide: Basal cell adhesion molecule
    • Protein or peptide: Laminin subunit alpha-5
    • Protein or peptide: Laminin subunit beta-1
    • Protein or peptide: Laminin subunit gamma-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Laminin 511 in complex with BCAM

SupramoleculeName: Laminin 511 in complex with BCAM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4, #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Laminin subunit beta-1

MacromoleculeName: Laminin subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.688816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YPYDVPDYAG GSLQHSAADI ARAEMLLEEA KRASKSATDV KVTADMVKEA LEEAEKAQVA AEKAIKQADE DIQGTQNLLT SIESETAAS EETLFNASQR ISELERNVEE LKRKAAQNSG EAEYIEKVVY TVKQSAEDVK KTLDGELDEK YKKVENLIAK K TEESADAR ...String:
YPYDVPDYAG GSLQHSAADI ARAEMLLEEA KRASKSATDV KVTADMVKEA LEEAEKAQVA AEKAIKQADE DIQGTQNLLT SIESETAAS EETLFNASQR ISELERNVEE LKRKAAQNSG EAEYIEKVVY TVKQSAEDVK KTLDGELDEK YKKVENLIAK K TEESADAR RKAEMLQNEA KTLLAQANSK LQLLKDLERK YEDNQRYLED KAQELARLEG EVRSLLKDIS QKVAVYSTCL

UniProtKB: Laminin subunit beta-1

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Macromolecule #2: Laminin subunit gamma-1

MacromoleculeName: Laminin subunit gamma-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.47067 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NDILNNLKDF DRRVNDNKTA AEEALRKIPA INQTITEANE KTREAQQALG SAAADATEAK NKAHEAERIA SAVQKNATST KAEAERTFA EVTDLDNEVN NMLKQLQEAE KELKRKQDDA DQDMMMAGMA SQAAQEAEIN ARKAKNSVTS LLSIINDLLE Q LGQLDTVD ...String:
NDILNNLKDF DRRVNDNKTA AEEALRKIPA INQTITEANE KTREAQQALG SAAADATEAK NKAHEAERIA SAVQKNATST KAEAERTFA EVTDLDNEVN NMLKQLQEAE KELKRKQDDA DQDMMMAGMA SQAAQEAEIN ARKAKNSVTS LLSIINDLLE Q LGQLDTVD LNKLNEIEGT LNKAKDEMKV SDLDRKVSDL ENEAKKQEAA IMDYNRDIEE IMKCIRNLED IRKTLPSGCF NT PSIEKP

UniProtKB: Laminin subunit gamma-1

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Macromolecule #3: Basal cell adhesion molecule

MacromoleculeName: Basal cell adhesion molecule / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.74409 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AEVRLSVPPL VEVMRGKSVI LDCTPTGTHD HYMLEWFLTD RSGARPRLAS AEMQGSELQV TMHDTRGRSP PYQLDSQGRL VLAEAQVGD ERDYVCVVRA GAAGTAEATA RLNVFAKPEA TEVSPNKGTL SVMEDSAQEI ATCNSRNGNP APKITWYRNG Q RLEVPVEM ...String:
AEVRLSVPPL VEVMRGKSVI LDCTPTGTHD HYMLEWFLTD RSGARPRLAS AEMQGSELQV TMHDTRGRSP PYQLDSQGRL VLAEAQVGD ERDYVCVVRA GAAGTAEATA RLNVFAKPEA TEVSPNKGTL SVMEDSAQEI ATCNSRNGNP APKITWYRNG Q RLEVPVEM NPEGYMTSRT VREASGLLSL TSTLYLRLRK DDRDASFHCA AHYSLPEGRH GRLDSPTFHL TLHYPTEHVQ FW VGSPSTP AGWVREGDTV QLLCRGDGSP SPEYTLFRLQ DEQEEVLNVN LEGNLTLEGV TRGQSGTYGC RVEDYDAADD VQL SKTLEL RVAYLDPLEL SEGKVLSLPL NSSAVVNCSV HGLPTPALRW TKDSTPLGDG PMLSLSSITF DSNGTYVCEA SLPT VPVLS RTQNFTLLVQ GSPELKTAEI EPKADGSWRE GDEVTLICSA RGHPDPKLSW SQLGGSPAEP IPGRQGWVSS SLTLK VTSA LSRDGISCEA SNPHGNKRHV FHFGTVS

UniProtKB: Basal cell adhesion molecule

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Macromolecule #4: Laminin subunit alpha-5

MacromoleculeName: Laminin subunit alpha-5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.477898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAEDAAGQAL QQADHTWATV VRQGLVDRAQ QLLANSTALE EAMLQEQQRL GLVWAALQGA RTQLRDVRAK KDQLEAHIQA AQAMLAMDT DETSKKIAHA KAVAAEAQDT ATRVQSQLQA MQENVERWQG QYEGLRGQDL GQAVLDAGHS VSTLEKTLPQ L LAKLSILE ...String:
AAEDAAGQAL QQADHTWATV VRQGLVDRAQ QLLANSTALE EAMLQEQQRL GLVWAALQGA RTQLRDVRAK KDQLEAHIQA AQAMLAMDT DETSKKIAHA KAVAAEAQDT ATRVQSQLQA MQENVERWQG QYEGLRGQDL GQAVLDAGHS VSTLEKTLPQ L LAKLSILE NRGVHNASLA LSASIGRVRE LIAQARGAAS KVKVPMKFNG RSGVQLRTPR DLADLAAYTA LKFYLQGPEP EP GQGTEDR FVMYMGSRQA TGDYMGVSLR DKKVHWVYQL GEAGPAVLSI DEDIGEQFAA VSLDRTLQFG HMSVTVERQM IQE TKGDTV APGAEGLLNL RPDDFVFYVG GYPSTFTPPP LLRFPGYRGC IEMDTLNEEV VSLYNFERTF QLDTAVDRPC ARSK STGDP WLTDGSYLDG TGFARISFDS QISTTKRFEQ ELRLVSYSGV LFFLKQQSQF LCLAVQEGSL VLLYDFGAGL KKAVP LQPP PPLTSASKAI QVFLLGGSRK RVLVRVERAT VYSVEQDNDL ELADAYYLGG VPPDQLPPSL RRLFPTGGSV RGCVKG IKA LGKYVDLKRL NTTGVSAGCT ADLLVGRAMT FHGHGFLRLA LSNVAPLTGN VYSGFGFHSA QDSALLYYRA SPDGLCQ VS LQQGRVSLQL LRTEVKTQAG FADGAPHYVA FYSNATGVWL YVDDQLQQMK PHRGPPPELQ PQPEGPPRLL LGGLPESG T IYNFSGCISN VFVQRLLGPQ RVFDLQQNLG SVNVSTGCAP ALQAQTPGLG PRGLQATARK ASRRSRQPAR HPA

UniProtKB: Laminin subunit alpha-5

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / 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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3190706 / Details: Autopick
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 525751
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3) / Details: Ab initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3) / Details: Non uniform refinement

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