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- PDB-9hmh: Crystal structure of the Calf domains of Integrin Alpha5 -

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Basic information

Entry
Database: PDB / ID: 9hmh
TitleCrystal structure of the Calf domains of Integrin Alpha5
ComponentsIntegrin alpha-5
KeywordsSIGNALING PROTEIN / Integrin / alpha5-integrin / angiopoietin-2 / ANGPT2
Function / homology
Function and homology information


integrin alpha5-beta1 complex / cell-cell adhesion mediated by integrin / CD40 signaling pathway / RUNX2 regulates genes involved in cell migration / Fibronectin matrix formation / alphav-beta3 integrin-vitronectin complex / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of cell-substrate adhesion / Elastic fibre formation ...integrin alpha5-beta1 complex / cell-cell adhesion mediated by integrin / CD40 signaling pathway / RUNX2 regulates genes involved in cell migration / Fibronectin matrix formation / alphav-beta3 integrin-vitronectin complex / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of cell-substrate adhesion / Elastic fibre formation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / wound healing, spreading of epidermal cells / heterophilic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / heterotypic cell-cell adhesion / epidermal growth factor receptor binding / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / leukocyte cell-cell adhesion / response to muscle activity / positive regulation of sprouting angiogenesis / cell-substrate adhesion / endodermal cell differentiation / negative regulation of anoikis / Integrin cell surface interactions / ruffle / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Cell surface interactions at the vascular wall / negative regulation of autophagy / Signal transduction by L1 / integrin-mediated signaling pathway / female pregnancy / cell-cell adhesion / integrin binding / autophagy / memory / GPER1 signaling / virus receptor activity / signaling receptor activity / angiogenesis / cytoplasmic vesicle / postsynaptic membrane / cell adhesion / positive regulation of cell migration / external side of plasma membrane / focal adhesion / calcium ion binding / glutamatergic synapse / cell surface / endoplasmic reticulum / Golgi apparatus / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / 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 ...: / Integrin alpha Ig-like domain 3 / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMurthy, A.V. / Sipila, T.J.O. / Ponna, S.K. / Leppanen, V.M.L. / Saharinen, P.I.
Funding supportEuropean Union, Finland, 6items
OrganizationGrant numberCountry
European Research Council (ERC)773076European Union
Sigrid Juselius Foundation Finland
Academy of Finland310075 Finland
Academy of Finland346134 Finland
Other privateJenny and Antti Wihuri Foundation
Other privateCancer Foundation Finland
CitationJournal: To Be Published
Title: Angiopoietin-2 interactions with active vs inactive alpha5beta1-integrin at cell-cell junctions determine TIE2-FOXO1 pathway activation
Authors: Sipila, T. / Murthy, A.V. / Ponna, S.K. / Pink, A. / Enkavi, G. / Vattulainen, I. / Leppanen, V.M. / Saharinen, P.
History
DepositionDec 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: 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-5


Theoretical massNumber of molelcules
Total (without water)40,2511
Polymers40,2511
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16990 Å2
Unit cell
Length a, b, c (Å)50.016, 71.437, 121.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40251.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Integrin alpha5 calf domains / Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA5, FNRA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P08648
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density meas: 3.5 Mg/m3 / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bistris pH 5.5, 0.2M MgCl2, 25% PEG 3350 (wt/vol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→46.28 Å / Num. obs: 33875 / % possible obs: 99.5 % / Redundancy: 19.8 % / CC1/2: 0.995 / Rrim(I) all: 0.15 / Net I/σ(I): 5.47
Reflection shellResolution: 1.97→2.05 Å / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7412 / CC1/2: 0.14 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→46.28 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.074 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2822 1995 5.903 %
Rwork0.2218 31802 -
all0.225 --
obs-33797 99.485 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.034 Å2-0 Å20 Å2
2--3.139 Å2-0 Å2
3----0.105 Å2
Refinement stepCycle: LAST / Resolution: 1.92→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 188 2716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122585
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162421
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.6493512
X-RAY DIFFRACTIONr_angle_other_deg0.7571.5695582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2225318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.935514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71510430
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2910128
X-RAY DIFFRACTIONr_chiral_restr0.1030.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023048
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02588
X-RAY DIFFRACTIONr_nbd_refined0.2230.2515
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22314
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21147
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2176
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.213
X-RAY DIFFRACTIONr_nbd_other0.2090.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.29
X-RAY DIFFRACTIONr_mcbond_it6.4244.91281
X-RAY DIFFRACTIONr_mcbond_other6.4244.9011281
X-RAY DIFFRACTIONr_mcangle_it8.8038.7891596
X-RAY DIFFRACTIONr_mcangle_other8.8028.7921597
X-RAY DIFFRACTIONr_scbond_it7.7775.7751304
X-RAY DIFFRACTIONr_scbond_other7.7755.7771305
X-RAY DIFFRACTIONr_scangle_it11.12510.241916
X-RAY DIFFRACTIONr_scangle_other11.12310.2421917
X-RAY DIFFRACTIONr_lrange_it31.12458.2822805
X-RAY DIFFRACTIONr_lrange_other30.99657.3322789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.92-1.970.4451440.41822940.4224540.8340.83799.3480.415
1.97-2.0240.3781420.37422680.37524100.870.8561000.366
2.024-2.0820.4521400.36822210.37223640.8160.85899.87310.357
2.082-2.1460.3991310.32621100.3322490.8360.89699.64430.314
2.146-2.2160.3181300.29820770.29922130.9140.92399.72890.277
2.216-2.2940.3291280.27720180.2821510.9150.93599.76750.245
2.294-2.380.3051220.24619470.2520800.9410.95699.47120.215
2.38-2.4770.3061170.2618600.26319820.940.95399.74770.223
2.477-2.5870.311110.24717760.25118990.9280.95799.36810.21
2.587-2.7130.3211080.22917260.23518480.9340.96699.24240.195
2.713-2.8590.2961040.22616500.23117630.9430.96599.48950.194
2.859-3.0320.334970.21415500.2216550.9250.9799.51660.186
3.032-3.240.275920.20614760.2115720.9510.97299.74550.188
3.24-3.4980.278860.21613640.2214520.9580.97499.86230.205
3.498-3.830.251810.20412820.20713700.9540.97799.48910.199
3.83-4.2790.25720.17611430.1812270.9630.98199.0220.181
4.279-4.9330.221640.15410270.15811050.9680.98698.7330.169
4.933-6.0250.273540.1938710.1979480.9640.98197.57380.216
6.025-8.4490.228450.2087070.217570.970.97299.33950.226
8.449-46.280.243270.2294340.234680.9680.96398.50430.272

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