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- PDB-9hmi: Crystal structure of the Calf domains of Integrin Alpha5 in compl... -

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Basic information

Entry
Database: PDB / ID: 9hmi
TitleCrystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2 peptide
Components
  • Angiopoietin-2
  • Integrin alpha-5
KeywordsSIGNALING PROTEIN / Integrin / alpha5-integrin / angiopoietin-2 / ANGPT2
Function / homology
Function and homology information


negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / integrin alpha5-beta1 complex / cell-cell adhesion mediated by integrin / positive regulation of coagulation / CD40 signaling pathway / RUNX2 regulates genes involved in cell migration / Fibronectin matrix formation / alphav-beta3 integrin-vitronectin complex ...negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / integrin alpha5-beta1 complex / cell-cell adhesion mediated by integrin / positive regulation of coagulation / 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 / germ cell development / negative regulation of blood vessel endothelial cell migration / negative regulation of anoikis / negative regulation of cell-substrate adhesion / animal organ regeneration / maternal process involved in female pregnancy / Integrin cell surface interactions / response to mechanical stimulus / response to glucose / ruffle / cell projection / Tie2 Signaling / negative regulation of angiogenesis / 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 / response to activity / negative regulation of autophagy / Signal transduction by L1 / integrin-mediated signaling pathway / female pregnancy / cell-cell adhesion / receptor tyrosine kinase binding / integrin binding / cellular response to growth factor stimulus / autophagy / memory / positive regulation of angiogenesis / blood coagulation / GPER1 signaling / virus receptor activity / signaling receptor activity / angiogenesis / cytoplasmic vesicle / gene expression / response to hypoxia / postsynaptic membrane / cell adhesion / positive regulation of cell migration / receptor ligand activity / signaling receptor binding / external side of plasma membrane / focal adhesion / calcium ion binding / glutamatergic synapse / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / : / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / ANG-1-like domain / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal ...: / ANG-1-like domain / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / : / 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
Angiopoietin-2 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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
P: Angiopoietin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4803
Polymers41,2582
Non-polymers2211
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint1 kcal/mol
Surface area19630 Å2
Unit cell
Length a, b, c (Å)49.977, 69.231, 137.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA5, FNRA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P08648
#2: Protein/peptide Angiopoietin-2 / ANG-2


Mass: 1007.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15123
#3: 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.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.55 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium formate; 20% polyethylene glycol 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: 0.99 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.78→48.84 Å / Num. obs: 12325 / % possible obs: 97.6 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.21 / Net I/σ(I): 7.3
Reflection shellResolution: 2.78→2.93 Å / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1511 / CC1/2: 0.15 / Rpim(I) all: 0.9 / Rrim(I) all: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→48.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 21.961 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R: 1.3 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.306 610 5 %RANDOM
Rwork0.204 ---
obs0.203 11669 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---1.05 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.78→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 15 108 2896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122847
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162646
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.653868
X-RAY DIFFRACTIONr_angle_other_deg0.631.5716105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2635353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.718517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42510471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it17.67111.3341418
X-RAY DIFFRACTIONr_mcbond_other17.60611.3381418
X-RAY DIFFRACTIONr_mcangle_it24.04120.3171769
X-RAY DIFFRACTIONr_mcangle_other24.03820.3211770
X-RAY DIFFRACTIONr_scbond_it19.20812.0131429
X-RAY DIFFRACTIONr_scbond_other19.20112.0141430
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other27.38421.7042100
X-RAY DIFFRACTIONr_long_range_B_refined31.8656.9123201
X-RAY DIFFRACTIONr_long_range_B_other31.8656.9123202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 26 -
Rwork0.424 590 -
obs--68.14 %

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