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- PDB-9p6s: Cryo-EM structure of human integrin alpha5beta1 in complex with f... -

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Basic information

Entry
Database: PDB / ID: 9p6s
TitleCryo-EM structure of human integrin alpha5beta1 in complex with fibronectin (FN 7-10)
Components
  • Fibronectin
  • Integrin alpha-5
  • Integrin beta-1
KeywordsCELL ADHESION / a5b1 integrin / fibronectin / extracellular matrix / focal adhesion / single-particle
Function / homology
Function and homology information


integrin alpha8-beta1 complex / myoblast fate specification / integrin alpha3-beta1 complex / integrin alpha5-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 / integrin alpha9-beta1 complex ...integrin alpha8-beta1 complex / myoblast fate specification / integrin alpha3-beta1 complex / integrin alpha5-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 / integrin alpha9-beta1 complex / cardiac cell fate specification / regulation of collagen catabolic process / cell adhesion receptor activity / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / 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 / negative regulation of monocyte activation / Other semaphorin interactions / Formation of the ureteric bud / negative regulation of transforming growth factor beta production / cerebellar climbing fiber to Purkinje cell synapse / positive regulation of substrate-dependent cell migration, cell attachment to substrate / CD40 signaling pathway / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / reactive gliosis / positive regulation of fibroblast growth factor receptor signaling pathway / myelin sheath abaxonal region / integrin alphav-beta1 complex / CHL1 interactions / regulation of synapse pruning / fibrinogen complex / basement membrane organization / cardiac muscle cell myoblast differentiation / RUNX2 regulates genes involved in cell migration / Fibronectin matrix formation / Attachment of bacteria to epithelial cells / alphav-beta3 integrin-vitronectin complex / MET interacts with TNS proteins / Laminin interactions / Developmental Lineage of Mammary Stem Cells / enteric nervous system development / Platelet Adhesion to exposed collagen / integrin activation / germ cell migration / leukocyte tethering or rolling / vascular endothelial growth factor receptor 2 binding / ALK mutants bind TKIs / cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial growth factor signaling pathway / myoblast fusion / positive regulation of cell-substrate adhesion / cardiac muscle cell differentiation / Elastic fibre formation / cell-substrate junction assembly / axon extension / platelet-derived growth factor receptor binding / myoblast differentiation / mesodermal cell differentiation / central nervous system neuron differentiation / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / proteoglycan binding / cell projection organization / positive regulation of vascular endothelial growth factor receptor signaling pathway / wound healing, spreading of epidermal cells / heterophilic cell-cell adhesion / positive regulation of fibroblast migration / integrin complex / regulation of spontaneous synaptic transmission / negative regulation of Rho protein signal transduction / cell adhesion mediated by integrin / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / MET activates PTK2 signaling / Basigin interactions / epidermal growth factor receptor binding / lamellipodium assembly / peptidase activator activity / neural crest cell migration / negative regulation of vasoconstriction / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / muscle organ development / sarcomere organization / leukocyte cell-cell adhesion / Syndecan interactions / extracellular matrix structural constituent / biological process involved in interaction with symbiont / p130Cas linkage to MAPK signaling for integrins / positive regulation of neuroblast proliferation / dendrite morphogenesis / positive regulation of wound healing / negative regulation of neuron differentiation / response to muscle activity / positive regulation of sprouting angiogenesis / regulation of protein phosphorylation
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain / : / 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 / Kringle-like fold / Fibronectin type III domain / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Fibronectin / Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsDing, J. / Fantini, D. / Dedden, D. / Schumacher, S. / Biertumpfel, C. / Mizuno, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1ZIAHL006264 United States
CitationJournal: Pnas Nexus / Year: 2026
Title: Allosteric regulation of fibronectin binding by the anti-beta 1 integrin antibody TS2/16.
Authors: Ding, J. / Fantini, D.A. / Dedden, D. / Schumacher, S. / Biertumpfel, C. / Mizuno, N.
History
DepositionJun 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-5
B: Integrin beta-1
C: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,27621
Polymers133,5353
Non-polymers5,74118
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, negative-staining EM, assay for oligomerization, size-exclusion chromatography (SEC), light scattering, dynamic light-scattering (DLS), light scattering, size-exclusion ...Evidence: electron microscopy, negative-staining EM, assay for oligomerization, size-exclusion chromatography (SEC), light scattering, dynamic light-scattering (DLS), light scattering, size-exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALS), assay for oligomerization, sucrose gradient centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Integrin alpha-5 / CD49 antigen-like family member E / Fibronectin receptor subunit alpha / Integrin alpha-F / VLA-5


Mass: 64733.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: processed (signal peptide is cleaved) / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P08648
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 48952.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: processed (signal peptide is cleaved) / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P05556
#3: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 19849.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: truncated to domains FN7-10 / Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P02751

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Sugars , 5 types, 11 molecules

#4: 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.: 3
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
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#7: 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.: 2 / Source method: obtained synthetically
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
#9: 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.: 4 / Source method: isolated from a natural 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, 34 molecules

#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: integrin a5b1-fibronectin complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: placenta
Buffer solutionpH: 7.5
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: integrin a5b1 in nanodiscs (MSPE3D1) was incubated with 10 mM MnCl2 for 30 min at 4C, then mixed with purified FN7-10 at a molar ratio of 1:3, at a final a5b1-ND concentration of 0.15 mg/ml ...Details: integrin a5b1 in nanodiscs (MSPE3D1) was incubated with 10 mM MnCl2 for 30 min at 4C, then mixed with purified FN7-10 at a molar ratio of 1:3, at a final a5b1-ND concentration of 0.15 mg/ml in TBS pH 7.5 and 1 mM MnCl2.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 105000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 500 nm / Cs: 2.62 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 69 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10341
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4RELION3CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELIONclassification
13RELION33D reconstruction
14Cootmodel refinement
15PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2640989
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130907 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: initial rigid body fitting in chimera, then cycles of manual adjustment/modeling in coot and real-space refinement in phenix
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-IDChain residue rangePdb chain residue range
13vi3

3vi3

3vi31
21fnf

1fnf

1fnf21327-15091327-1509
RefinementHighest resolution: 2.61 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039956
ELECTRON MICROSCOPYf_angle_d0.69313524
ELECTRON MICROSCOPYf_dihedral_angle_d12.4411840
ELECTRON MICROSCOPYf_chiral_restr0.051570
ELECTRON MICROSCOPYf_plane_restr0.0051742

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