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- PDB-9dia: Cryo-EM structure of alpha5beta1 integrin in complex with NeoNect... -

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Basic information

Entry
Database: PDB / ID: 9dia
TitleCryo-EM structure of alpha5beta1 integrin in complex with NeoNectin candidate 2
Components
  • Integrin alpha-5
  • Integrin beta-1
  • NeoNectin candidate 2
KeywordsSIGNALING PROTEIN / a5B1 / de novo / tissue regeneration / extracellular matrix protein
Function / homology
Function and homology information


integrin alpha8-beta1 complex / 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 / myoblast fate specification / integrin alpha9-beta1 complex ...integrin alpha8-beta1 complex / 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 / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / myelin sheath abaxonal region / CD40 signaling pathway / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of synapse pruning / integrin alphav-beta1 complex / CHL1 interactions / basement membrane organization / RUNX2 regulates genes involved in cell migration / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / alphav-beta3 integrin-vitronectin complex / Laminin interactions / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / germ cell migration / leukocyte tethering or rolling / vascular endothelial growth factor receptor 2 binding / cell projection organization / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of vascular endothelial growth factor receptor signaling pathway / central nervous system neuron differentiation / positive regulation of cell-substrate adhesion / regulation of spontaneous synaptic transmission / heterophilic cell-cell adhesion / wound healing, spreading of epidermal cells / epidermal growth factor receptor binding / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / heterotypic cell-cell adhesion / sarcomere organization / MET activates PTK2 signaling / Basigin interactions / Molecules associated with elastic fibres / negative regulation of vasoconstriction / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / leukocyte cell-cell adhesion / muscle organ development / Syndecan interactions / cell adhesion mediated by integrin / positive regulation of wound healing / dendrite morphogenesis / negative regulation of neuron differentiation / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / response to muscle activity / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / cell-substrate adhesion / homophilic cell-cell adhesion / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / cleavage furrow / establishment of mitotic spindle orientation / fibronectin binding / negative regulation of anoikis / intercalated disc / cellular response to low-density lipoprotein particle stimulus / RHOG GTPase cycle / positive regulation of GTPase activity / glial cell projection / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / ECM proteoglycans
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / 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 alpha, N-terminal / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1.
Similarity search - Domain/homology
: / Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsWerther, R. / Nguyen, A. / Estrada Alamo, K.A. / Wang, X. / Campbell, M.G.
Funding support United States, 4items
OrganizationGrant numberCountry
The Pew Charitable TrustsNA United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM147414-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA015704-40; RRID:SCR_022611 United States
Other privateSeattle Cancer Consortium Safeway Inc Pilot Grant
CitationJournal: Adv Mater / Year: 2025
Title: De Novo Design of Integrin α5β1 Modulating Proteins to Enhance Biomaterial Properties.
Authors: Xinru Wang / Jordi Guillem-Marti / Saurav Kumar / David S Lee / Daniel Cabrerizo-Aguado / Rachel Werther / Kevin Alexander Estrada Alamo / Yan Ting Zhao / Adam Nguyen / Irina Kopyeva / Buwei ...Authors: Xinru Wang / Jordi Guillem-Marti / Saurav Kumar / David S Lee / Daniel Cabrerizo-Aguado / Rachel Werther / Kevin Alexander Estrada Alamo / Yan Ting Zhao / Adam Nguyen / Irina Kopyeva / Buwei Huang / Jing Li / Yuxin Hao / Xinting Li / Aritza Brizuela-Velasco / Analisa Murray / Stacey Gerben / Anindya Roy / Cole A DeForest / Timothy Springer / Hannele Ruohola-Baker / Jonathan A Cooper / Melody G Campbell / Jose Maria Manero / Maria-Pau Ginebra / David Baker /
Abstract: Integrin α5β1 is crucial for cell attachment and migration in development and tissue regeneration, and α5β1 binding proteins can have considerable utility in regenerative medicine and next- ...Integrin α5β1 is crucial for cell attachment and migration in development and tissue regeneration, and α5β1 binding proteins can have considerable utility in regenerative medicine and next-generation therapeutics. We use computational protein design to create de novo α5β1-specific modulating miniprotein binders, called NeoNectins, that bind to and stabilize the open state of α5β1. When immobilized onto titanium surfaces and throughout 3D hydrogels, the NeoNectins outperform native fibronectin (FN) and RGD peptides in enhancing cell attachment and spreading, and NeoNectin-grafted titanium implants outperformed FN- and RGD-grafted implants in animal models in promoting tissue integration and bone growth. NeoNectins should be broadly applicable for tissue engineering and biomedicine.
History
DepositionSep 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-5
B: Integrin beta-1
C: NeoNectin candidate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,52118
Polymers202,5923
Non-polymers3,92915
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
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: 109695.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA5, FNRA / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08648
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 81743.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1, FNRB, MDF2, MSK12 / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05556
#3: Protein NeoNectin candidate 2


Mass: 11152.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Sugars , 4 types, 10 molecules

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


Type: oligosaccharide / Mass: 951.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DGlcpNAcb1-4]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1/a4-b1_b4-c1_c3-d1_c4-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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.: 5 / Source method: obtained synthetically / 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, 5 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / 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: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin candidate 2
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2150 mMsodium chlorideNaCl1
31 mMmanganese chlorideMnCl21
SpecimenConc.: 0.09 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Details: Collection at 30 degrees tilt

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153759 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027052
ELECTRON MICROSCOPYf_angle_d0.4489592
ELECTRON MICROSCOPYf_dihedral_angle_d4.2051072
ELECTRON MICROSCOPYf_chiral_restr0.0421118
ELECTRON MICROSCOPYf_plane_restr0.0031234

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