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- PDB-9ckv: Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin -

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Basic information

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


integrin alpha8-beta1 complex / integrin alpha6-beta1 complex / regulation of inward rectifier potassium channel activity / integrin alpha3-beta1 complex / integrin alpha5-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 alpha8-beta1 complex / integrin alpha6-beta1 complex / regulation of inward rectifier potassium channel activity / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of collagen catabolic process / integrin alpha9-beta1 complex / cardiac cell fate specification / integrin alpha4-beta1 complex / integrin binding involved in cell-matrix adhesion / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / Formation of the ureteric bud / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / CD40 signaling pathway / basement membrane organization / myelin sheath abaxonal region / CHL1 interactions / alphav-beta3 integrin-vitronectin complex / RUNX2 regulates genes involved in cell migration / cardiac muscle cell myoblast differentiation / Laminin interactions / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / vascular endothelial growth factor receptor 2 binding / cell projection organization / Platelet Adhesion to exposed collagen / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / platelet-derived growth factor receptor binding / cell-substrate junction assembly / axon extension / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / myoblast differentiation / wound healing, spreading of epidermal cells / positive regulation of cell-substrate adhesion / regulation of spontaneous synaptic transmission / integrin complex / heterotypic cell-cell adhesion / Basigin interactions / dendrite morphogenesis / Molecules associated with elastic fibres / lamellipodium assembly / negative regulation of Rho protein signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / MET activates PTK2 signaling / negative regulation of vasoconstriction / epidermal growth factor receptor binding / Syndecan interactions / sarcomere organization / leukocyte cell-cell adhesion / positive regulation of wound healing / muscle organ development / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / endodermal cell differentiation / establishment of mitotic spindle orientation / TGF-beta receptor signaling activates SMADs / cleavage furrow / glial cell projection / fibronectin binding / negative regulation of anoikis / cellular response to low-density lipoprotein particle stimulus / intercalated disc / RHOG GTPase cycle / negative regulation of neuron differentiation / neuroblast proliferation / ECM proteoglycans / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / cellular defense response / phagocytosis
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / 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 / 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: 3.19 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: To Be Published
Title: De Novo Design of Integrin alpha5beta1 Modulating Proteins for Regenerative Medicine
Authors: Wang, X. / Guillem-Marti, J. / Kumar, S. / Lee, D.S. / Cabrerizo-Aguado, D. / Werther, R. / Estrada Alamo, K.A. / Zhao, Y.T. / Nguyen, A. / Kopyeva, I. / Huang, B. / Li, J. / Hao, Y. / Li, X. ...Authors: Wang, X. / Guillem-Marti, J. / Kumar, S. / Lee, D.S. / Cabrerizo-Aguado, D. / Werther, R. / Estrada Alamo, K.A. / Zhao, Y.T. / Nguyen, A. / Kopyeva, I. / Huang, B. / Li, J. / Hao, Y. / Li, X. / Brizuela-Velasco, A. / Murray, A.N. / Gerben, S. / Roy, A. / DeForest, C.A. / Springer, T. / Ruohola-Baker, H. / Cooper, J.A. / Campbell, M.G. / Maria Manero, J. / Ginebra, M. / Baker, D.
History
DepositionJul 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,83518
Polymers202,7113
Non-polymers4,12515
Water00
1


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

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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


Mass: 11270.766 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, 8 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.: 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
#5: 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.: 4
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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[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]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-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]{[(3+1)][a-D-Manp]{}}}}}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.: 2 / 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, 7 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: 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: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin
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: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2150 mMsodium chlorideNaCl1
31 mMmanganese chlorideMnCl21
SpecimenConc.: 0.1 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: 1200 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: 3 / Details: Collection at 30 degrees tilt

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72604 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 131.55 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00387034
ELECTRON MICROSCOPYf_angle_d0.56499548
ELECTRON MICROSCOPYf_chiral_restr0.04591104
ELECTRON MICROSCOPYf_plane_restr0.00381226
ELECTRON MICROSCOPYf_dihedral_angle_d5.99891078

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