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- PDB-21ir: Laminin 511 in complex with BCAM -

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Basic information

Entry
Database: PDB / ID: 21ir
TitleLaminin 511 in complex with BCAM
Components
  • (Laminin subunit ...) x 3
  • Basal cell adhesion molecule
KeywordsCELL ADHESION / Laminin 511 / BCAM
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhou, C. / Zheng, Y.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Laminin subunit beta-1
D: Laminin subunit gamma-1
A: Basal cell adhesion molecule
B: Laminin subunit alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,1896
Polymers196,3814
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Laminin subunit ... , 3 types, 3 molecules CDB

#1: Protein Laminin subunit beta-1 / Laminin B1 chain / Laminin-1 subunit beta / Laminin-10 subunit beta / Laminin-12 subunit beta / ...Laminin B1 chain / Laminin-1 subunit beta / Laminin-10 subunit beta / Laminin-12 subunit beta / Laminin-2 subunit beta / Laminin-6 subunit beta / Laminin-8 subunit beta


Mass: 26688.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMB1 / Production host: Homo sapiens (human) / References: UniProt: P07942
#2: Protein Laminin subunit gamma-1 / Laminin B2 chain / Laminin-1 subunit gamma / Laminin-10 subunit gamma / Laminin-11 subunit gamma / ...Laminin B2 chain / Laminin-1 subunit gamma / Laminin-10 subunit gamma / Laminin-11 subunit gamma / Laminin-2 subunit gamma / Laminin-3 subunit gamma / Laminin-4 subunit gamma / Laminin-6 subunit gamma / Laminin-7 subunit gamma / Laminin-8 subunit gamma / Laminin-9 subunit gamma / S-laminin subunit gamma / S-LAM gamma


Mass: 27470.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMC1, LAMB2 / Production host: Homo sapiens (human) / References: UniProt: P11047
#4: Protein Laminin subunit alpha-5 / Laminin-10 subunit alpha / Laminin-11 subunit alpha / Laminin-15 subunit alpha


Mass: 86477.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMA5, KIAA0533, KIAA1907 / Production host: Homo sapiens (human) / References: UniProt: O15230

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Protein , 1 types, 1 molecules A

#3: Protein Basal cell adhesion molecule / Auberger B antigen / B-CAM cell surface glycoprotein / F8/G253 antigen / Lutheran antigen / ...Auberger B antigen / B-CAM cell surface glycoprotein / F8/G253 antigen / Lutheran antigen / Lutheran blood group glycoprotein


Mass: 55744.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAM, LU, MSK19 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50895

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Sugars , 2 types, 2 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Laminin 511 in complex with BCAM / Type: COMPLEX / Entity ID: #3-#4, #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARC4.3CTF correction
10cryoSPARC4.3initial Euler assignment
11cryoSPARC4.3final Euler assignment
13cryoSPARC4.33D reconstruction
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3190706 / Details: Autopick
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 525751 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047312
ELECTRON MICROSCOPYf_angle_d0.7489911
ELECTRON MICROSCOPYf_dihedral_angle_d7.6381121
ELECTRON MICROSCOPYf_chiral_restr0.0511117
ELECTRON MICROSCOPYf_plane_restr0.0071294

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