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- PDB-9ri7: Integrin alpha(2) I-domain mutant -

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Basic information

Entry
Database: PDB / ID: 9ri7
TitleIntegrin alpha(2) I-domain mutant
ComponentsIntegrin alpha-2
KeywordsCELL ADHESION / Cell signaling / Rossmann fold / MIDAS / magnesium ion
Function / homology
Function and homology information


collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / skin morphogenesis ...collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / skin morphogenesis / CHL1 interactions / response to L-ascorbic acid / collagen-activated signaling pathway / positive regulation of smooth muscle contraction / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / hepatocyte differentiation / positive regulation of phagocytosis, engulfment / focal adhesion assembly / mammary gland development / heparan sulfate proteoglycan binding / mesodermal cell differentiation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / response to amine / integrin complex / cell adhesion mediated by integrin / MET activates PTK2 signaling / positive regulation of smooth muscle cell migration / Syndecan interactions / response to muscle activity / cell-substrate adhesion / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / ECM proteoglycans / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / collagen binding / extracellular matrix organization / laminin binding / positive regulation of cell adhesion / positive regulation of smooth muscle cell proliferation / axon terminus / animal organ morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / positive regulation of translation / cellular response to estradiol stimulus / female pregnancy / cellular response to mechanical stimulus / cell-cell adhesion / integrin binding / blood coagulation / amyloid-beta binding / virus receptor activity / signaling receptor activity / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / 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). ...: / Integrin alpha Ig-like domain 3 / 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 / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / SUCCINIC ACID / Integrin alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAirenne, T.T. / Bligt-Linden, E. / Parkash, V. / Kapyla, J. / Heino, J. / Salminen, T.A.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: To Be Published
Title: Integrin alpha(2) I-domain mutant
Authors: Airenne, T.T. / Bligt-Linden, E. / Parkash, V. / Kapyla, J. / Heino, J. / Salminen, T.A.
History
DepositionJun 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,81716
Polymers21,7741
Non-polymers1,04415
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.03, 53.76, 44.65
Angle α, β, γ (deg.)90, 100.62, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha


Mass: 21773.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301

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Non-polymers , 6 types, 170 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein solution (55 mg/ml): 40 mM Tris, pH 7.4, 2 mM MgCl2 Well solution: 0.1 M succinic acid, pH 7.0, 15 % PEG 3350 Drops: 2:1 ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 1.6→19.19 Å / Num. obs: 21566 / % possible obs: 94.6 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Rrim(I) all: 0.064 / Χ2: 1.01 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.76-19.193.30.01456.11310.9990.0140.0190.9288.3
1.6-1.6331.00418810.4151.0041.4191.1280

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Processing

Software
NameVersionClassification
XSCALEVERSION Jun 30, 2024 BUILT=20240723data scaling
AimlessVersion 0.8.2; no scaling, only mergedata scaling
PHASER2.8.3phasing
REFMAC5.8.0430 (refmacat 0.4.100)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.999 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2002 1084 5.026 %
Rwork0.1608 20482 -
all0.163 --
obs-21566 94.472 %
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: 21.839 Å2
Baniso -1Baniso -2Baniso -3
1--0.068 Å20 Å2-0.089 Å2
2---1.242 Å2-0 Å2
3---1.255 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 62 155 1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161563
X-RAY DIFFRACTIONr_angle_refined_deg2.271.8022154
X-RAY DIFFRACTIONr_angle_other_deg0.761.743586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.91257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61910269
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.8911069
X-RAY DIFFRACTIONr_chiral_restr0.1090.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.2180.2311
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21371
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2776
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2660.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1780.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.223
X-RAY DIFFRACTIONr_nbd_other0.1990.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.223
X-RAY DIFFRACTIONr_mcbond_it1.3361.179791
X-RAY DIFFRACTIONr_mcbond_other1.3261.177790
X-RAY DIFFRACTIONr_mcangle_it1.9862.113989
X-RAY DIFFRACTIONr_mcangle_other1.9862.114990
X-RAY DIFFRACTIONr_scbond_it2.831.498811
X-RAY DIFFRACTIONr_scbond_other2.8291.501812
X-RAY DIFFRACTIONr_scangle_it3.6332.5791161
X-RAY DIFFRACTIONr_scangle_other3.6312.581162
X-RAY DIFFRACTIONr_lrange_it5.58916.7821825
X-RAY DIFFRACTIONr_lrange_other5.41815.71789
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
1.6-1.6410.418530.37313090.37416480.9260.92482.64560.372
1.641-1.6860.396890.34714760.3516430.9150.93395.25260.34
1.686-1.7340.293760.33614210.33415850.9480.9494.44790.325
1.734-1.7870.351690.30713810.30915380.9330.94894.27830.29
1.787-1.8450.301730.29113090.29114890.9450.95192.8140.266
1.845-1.910.286680.25212400.25414310.950.96391.40460.22
1.91-1.9810.326580.20312560.20814090.9390.97493.25760.177
1.981-2.0610.231640.17511920.17813310.9710.98294.36510.152
2.061-2.1510.206700.16311560.16612930.9780.98494.81830.145
2.151-2.2550.232630.1610990.16412280.9580.98594.62540.148
2.255-2.3750.206500.1310740.13311720.9770.99195.90440.119
2.375-2.5170.153510.11310400.11511220.9890.99397.23710.107
2.517-2.6870.137590.1069740.10810550.9890.99497.91470.1
2.687-2.8980.148470.1079140.1099710.9840.99398.97010.104
2.898-3.1670.143420.1148530.1169150.9860.99297.81420.11
3.167-3.5290.142410.1187640.128110.9880.99299.26020.119
3.529-4.0520.157300.1146990.1157380.9880.99298.78050.117
4.052-4.9090.132340.1115730.1136230.9910.99397.43180.12
4.909-6.7260.269300.224590.2224940.9680.98298.98790.23
6.726-19.190.215170.2012930.2013170.9870.98897.79180.215
Refinement TLS params.Method: refined / Origin x: -6.8843 Å / Origin y: 4.7372 Å / Origin z: -12.6855 Å
111213212223313233
T0.0118 Å2-0.0035 Å2-0.0143 Å2-0.0888 Å20.0128 Å2--0.0261 Å2
L1.0677 °20.0082 °2-0.0463 °2-1.3557 °20.255 °2--0.6118 °2
S0.0144 Å °-0.052 Å °0.0045 Å °0.105 Å °-0.0116 Å °-0.0736 Å °0.0163 Å °0.0456 Å °-0.0028 Å °
Refinement TLS groupSelection: ALL

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