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- PDB-7cec: Structure of alpha6beta1 integrin in complex with laminin-511 -

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Basic information

Entry
Database: PDB / ID: 7cec
TitleStructure of alpha6beta1 integrin in complex with laminin-511
Components
  • (Laminin subunit ...) x 3
  • HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH
  • HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)
  • Integrin alpha-6
  • Integrin beta-1
  • TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH
  • TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)
KeywordsCELL ADHESION/IMMUNE SYSTEM / Integrin / Laminin / Fv-clasp / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


integrin alpha6-beta4 complex / laminin-522 trimer / laminin-523 trimer / laminin-332 trimer / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-411 trimer / laminin-521 trimer / laminin-211 trimer / Developmental Lineage of Mammary Gland Alveolar Cells / Developmental Lineage of Mammary Gland Luminal Epithelial Cells ...integrin alpha6-beta4 complex / laminin-522 trimer / laminin-523 trimer / laminin-332 trimer / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-411 trimer / laminin-521 trimer / laminin-211 trimer / Developmental Lineage of Mammary Gland Alveolar Cells / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / laminin-111 trimer / laminin-511 trimer / regulation of basement membrane organization / integrin alpha8-beta1 complex / neuregulin binding / myoblast fate specification / extracellular matrix of synaptic cleft / L1CAM interactions / integrin alpha3-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / Type I hemidesmosome assembly / cardiac cell fate specification / integrin alpha5-beta1 complex / integrin alpha9-beta1 complex / ectodermal cell differentiation / regulation of collagen catabolic process / nail development / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / hemidesmosome assembly / integrin alpha4-beta1 complex / cell adhesion receptor activity / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / cell-cell adhesion mediated by integrin / formation of radial glial scaffolds / glycosphingolipid binding / Other semaphorin interactions / positive regulation of integrin-mediated signaling pathway / Formation of the ureteric bud / cerebellar climbing fiber to Purkinje cell synapse / postsynapse organization / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / reactive gliosis / myelin sheath abaxonal region / integrin alphav-beta1 complex / basement membrane organization / skin morphogenesis / CHL1 interactions / cardiac muscle cell myoblast differentiation / regulation of synapse pruning / Fibronectin matrix formation / Attachment of bacteria to epithelial cells / MET interacts with TNS proteins / protein complex involved in cell-matrix adhesion / Laminin interactions / Developmental Lineage of Mammary Stem Cells / primordial germ cell migration / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Platelet Adhesion to exposed collagen / endoderm development / leukocyte tethering or rolling / Formation of the dystrophin-glycoprotein complex (DGC) / insulin-like growth factor I binding / negative regulation of cell adhesion / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / cell migration involved in sprouting angiogenesis / axon extension / Elastic fibre formation / cardiac muscle cell differentiation / cell-substrate junction assembly / myoblast differentiation / mesodermal cell differentiation / central nervous system neuron differentiation / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / cell projection organization / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / Assembly of collagen fibrils and other multimeric structures / negative regulation of Rho protein signal transduction / odontogenesis / integrin complex / regulation of spontaneous synaptic transmission / skeletal system morphogenesis / cell adhesion mediated by integrin / Molecules associated with elastic fibres / MET activates PTK2 signaling / heterotypic cell-cell adhesion / leukocyte migration / Basigin interactions / lamellipodium assembly / negative regulation of vasoconstriction
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 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 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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / : / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / Epidermal growth factor-like domain. / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Laminin subunit alpha-5 / Integrin beta-1 / Laminin subunit beta-1 / Laminin subunit gamma-1 / Integrin alpha-6
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsArimori, T. / Miyazaki, N. / Takagi, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02389 Japan
Japan Agency for Medical Research and Development (AMED)19am0101075 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structural mechanism of laminin recognition by integrin.
Authors: Takao Arimori / Naoyuki Miyazaki / Emiko Mihara / Mamoru Takizawa / Yukimasa Taniguchi / Carlos Cabañas / Kiyotoshi Sekiguchi / Junichi Takagi /
Abstract: Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we ...Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we report the structures of the prototypic laminin receptor α6β1 integrin alone and in complex with three-chain laminin-511 fragment determined via crystallography and cryo-electron microscopy, respectively. The laminin-integrin interface is made up of several binding sites located on all five subunits, with the laminin γ1 chain C-terminal portion providing focal interaction using two carboxylate anchor points to bridge metal-ion dependent adhesion site of integrin β1 subunit and Asn189 of integrin α6 subunit. Laminin α5 chain also contributes to the affinity and specificity by making electrostatic interactions with large surface on the β-propeller domain of α6, part of which comprises an alternatively spliced X1 region. The propeller sheet corresponding to this region shows unusually high mobility, suggesting its unique role in ligand capture.
History
DepositionJun 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Integrin alpha-6
B: Integrin beta-1
C: Laminin subunit alpha-5
D: Laminin subunit beta-1
E: Laminin subunit gamma-1
F: TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH
G: TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)
H: HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH
I: HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,01023
Polymers286,9349
Non-polymers2,07714
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24140 Å2
ΔGint-113 kcal/mol
Surface area93980 Å2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-6 / CD49 antigen-like family member F / VLA-6


Mass: 69776.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA6 / Production host: Homo sapiens (human) / References: UniProt: P23229
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 50510.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1, FNRB, MDF2, MSK12 / Production host: Homo sapiens (human) / References: UniProt: P05556

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Laminin subunit ... , 3 types, 3 molecules CDE

#3: Protein Laminin subunit alpha-5 / Laminin-10 subunit alpha / Laminin-11 subunit alpha / Laminin-15 subunit alpha


Mass: 73414.203 Da / Num. of mol.: 1 / Fragment: E8 fragment / Mutation: I2723C
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
#4: 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: 8552.753 Da / Num. of mol.: 1 / Fragment: E8 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMB1 / Production host: Homo sapiens (human) / References: UniProt: P07942
#5: 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: 9483.724 Da / Num. of mol.: 1 / Fragment: E8 fragment / Mutation: D1585C
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

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Antibody , 4 types, 4 molecules FGHI

#6: Antibody TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH


Mass: 19463.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of TS2/16 VH(S112C)-SARAH
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#7: Antibody TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)


Mass: 18270.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of TS2/16 VL-SARAH(S37C)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#8: Antibody HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH


Mass: 19760.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of HUTS-4 VH(S112C)-SARAH
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#9: Antibody HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)


Mass: 17701.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of HUTS-4 VL(C87Y)-SARAH(S37C)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 7 molecules

#10: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#12: 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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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Non-polymers , 2 types, 7 molecules

#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#13: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn

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Details

Has ligand of interestN
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: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp
Type: COMPLEX / Entity ID: #1-#9 / Source: RECOMBINANT
Molecular weightValue: 0.286 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethaneC4H11NO31
2150 mMsodium chlorideNaCl1
31 mMmanganese chlorideMnCl21
40.1 mMcalcium chlorideCaCl21
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 800 nm / Nominal defocus min: 600 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7768
EM imaging opticsPhase plate: VOLTA PHASE PLATE
Image scansWidth: 4096 / Height: 4096

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2660283
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 429521 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010617940
ELECTRON MICROSCOPYf_angle_d1.201724302
ELECTRON MICROSCOPYf_chiral_restr0.07082689
ELECTRON MICROSCOPYf_plane_restr0.00783147
ELECTRON MICROSCOPYf_dihedral_angle_d16.348210854

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