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- PDB-8w30: Crystal structure of alpha-V beta-1 integrin headpiece in complex... -

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Basic information

Entry
Database: PDB / ID: 8w30
TitleCrystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179
Components
  • Integrin alpha-V heavy chain
  • Integrin beta-1
KeywordsCELL ADHESION / membrane receptor
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 binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / 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 / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / CD40 signaling pathway / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / integrin alphav-beta1 complex / regulation of synapse pruning / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / basement membrane organization / CHL1 interactions / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / leukocyte tethering or rolling / entry into host cell by a symbiont-containing vacuole / cardiac muscle cell differentiation / germ cell migration / alphav-beta3 integrin-PKCalpha complex / Platelet Adhesion to exposed collagen / cell projection organization / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / regulation of phagocytosis / Elastic fibre formation / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / myoblast differentiation / filopodium membrane / cell migration involved in sprouting angiogenesis / axon extension / extracellular matrix binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / negative regulation of low-density lipoprotein particle clearance / apolipoprotein A-I-mediated signaling pathway / central nervous system neuron differentiation / apoptotic cell clearance / integrin complex / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / regulation of spontaneous synaptic transmission / lamellipodium assembly / sarcomere organization / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative chemotaxis / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / Syndecan interactions / muscle organ development / positive regulation of wound healing / positive regulation of osteoblast proliferation / dendrite morphogenesis / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / negative regulation of Rho protein signal transduction / microvillus membrane / maintenance of blood-brain barrier / cell-substrate adhesion / response to muscle activity
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 EGF domain / Integrin beta subunit, tail ...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 EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrin alpha cytoplasmic region / 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 / 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 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-V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsQin, L. / Lane, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Design and Discovery of a Potent and Selective Inhibitor of Integrin alpha v beta 1.
Authors: Sabat, M. / Carney, D.W. / Hernandez-Torres, G. / Gibson, T.S. / Balakrishna, D. / Zou, H. / Xu, R. / Chen, C.H. / de Jong, R. / Dougan, D.R. / Qin, L. / Bigi-Botterill, S.V. / Chambers, A. ...Authors: Sabat, M. / Carney, D.W. / Hernandez-Torres, G. / Gibson, T.S. / Balakrishna, D. / Zou, H. / Xu, R. / Chen, C.H. / de Jong, R. / Dougan, D.R. / Qin, L. / Bigi-Botterill, S.V. / Chambers, A. / Miura, J. / Johnson, L.K. / Ermolieff, J. / Johns, D. / Selimkhanov, J. / Kwok, L. / DeMent, K. / Proffitt, C. / Vu, P. / Lindsey, E.A. / Ivetac, T. / Jennings, A. / Wang, H. / Manam, P. / Santos, C. / Fullenwider, C. / Manohar, R. / Flick, A.C.
History
DepositionFeb 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-V heavy chain
B: Integrin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,60016
Polymers117,2562
Non-polymers3,34414
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-11 kcal/mol
Surface area39870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.184, 148.212, 53.415
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-V heavy chain


Mass: 66498.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06756
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 50757.148 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05556

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Sugars , 3 types, 7 molecules

#3: 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
#4: 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
#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.: 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 , 3 types, 31 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-A1AFA / N-(2,4-dichlorobenzoyl)-L-phenylalanine


Mass: 338.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13Cl2NO3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% pentaerythritol ethoxylate (15/4_EO/OH), 0.05M ammonium sulfate, 0.05M Bis Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→48.48 Å / Num. obs: 51039 / % possible obs: 92.3 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rsym value: 0.069 / Net I/σ(I): 10.1
Reflection shellResolution: 2.45→2.53 Å / Redundancy: 3.7 % / Num. unique obs: 4394 / CC1/2: 0.453 / Rsym value: 2.389 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→47.875 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 2581 5.08 %
Rwork0.2549 --
obs0.256 50799 91.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→47.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7318 0 209 24 7551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047695
X-RAY DIFFRACTIONf_angle_d0.75510465
X-RAY DIFFRACTIONf_dihedral_angle_d14.5054584
X-RAY DIFFRACTIONf_chiral_restr0.0491193
X-RAY DIFFRACTIONf_plane_restr0.0041362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.49720.49891250.49492628X-RAY DIFFRACTION90
2.4972-2.54820.45611330.46042597X-RAY DIFFRACTION88
2.5482-2.60360.39441450.422360X-RAY DIFFRACTION83
2.6036-2.66410.46531340.40682610X-RAY DIFFRACTION87
2.6641-2.73080.43661410.3872729X-RAY DIFFRACTION95
2.7308-2.80460.39531390.37762827X-RAY DIFFRACTION95
2.8046-2.88710.38421430.34792713X-RAY DIFFRACTION95
2.8871-2.98030.41021340.3312798X-RAY DIFFRACTION95
2.9803-3.08680.3691150.32072757X-RAY DIFFRACTION94
3.0868-3.21040.37541390.31412722X-RAY DIFFRACTION93
3.2104-3.35640.36641360.31652726X-RAY DIFFRACTION93
3.3564-3.53330.34261530.28462638X-RAY DIFFRACTION91
3.5333-3.75460.37691090.26462419X-RAY DIFFRACTION82
3.7546-4.04440.27841470.25122729X-RAY DIFFRACTION93
4.0444-4.45110.24851730.21752792X-RAY DIFFRACTION96
4.4511-5.09460.20651670.18852779X-RAY DIFFRACTION96
5.0946-6.41620.21041870.21942691X-RAY DIFFRACTION93
6.4162-47.8750.22581610.20462703X-RAY DIFFRACTION91

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