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- PDB-4a0q: Activated Conformation of Integrin alpha1 I-Domain mutant -

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Basic information

Entry
Database: PDB / ID: 4a0q
TitleActivated Conformation of Integrin alpha1 I-Domain mutant
ComponentsINTEGRIN ALPHA-1
KeywordsCELL ADHESION / INTEGRIN
Function / homology
Function and homology information


integrin alpha1-beta1 complex / cellular extravasation / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / phosphatase activator activity / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex ...integrin alpha1-beta1 complex / cellular extravasation / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / phosphatase activator activity / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / Smooth Muscle Contraction / Integrin cell surface interactions / collagen binding / neutrophil chemotaxis / acrosomal vesicle / neuron projection morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / integrin binding / positive regulation of neuron apoptotic process / protein phosphatase binding / perikaryon / positive regulation of MAPK cascade / external side of plasma membrane / negative regulation of cell population proliferation / focal adhesion / cell surface / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 ...: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / 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 / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLahti, M. / Bligt, E. / Niskanen, H. / Parkash, V. / Brandt, A.-M. / Jokinen, J. / Patrikainen, P. / Kapyla, J. / Heino, J. / Salminen, T.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of Collagen Receptor Integrin Aplha1I Domain Carrying the Activating Mutation E317A.
Authors: Lahti, M. / Bligt, E. / Niskanen, H. / Parkash, V. / Brandt, A.M. / Jokinen, J. / Patrikainen, P. / Kapyla, J. / Heino, J. / Salminen, T.A.
History
DepositionSep 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRIN ALPHA-1
B: INTEGRIN ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7754
Polymers44,7262
Non-polymers492
Water3,315184
1
A: INTEGRIN ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3882
Polymers22,3631
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INTEGRIN ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3882
Polymers22,3631
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.470, 95.470, 37.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein INTEGRIN ALPHA-1 / CD49 ANTIGEN-LIKE FAMILY MEMBER A / LAMININ AND COLLAGEN RECEPTOR / VLA-1 / CD49A


Mass: 22363.223 Da / Num. of mol.: 2 / Fragment: INTEGRIN ALPHA1 I-DOMAIN, RESIDUES 166-366 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P56199
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 167 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 167 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 167 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 167 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 345 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 345 TO ALA

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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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 1.6 M TRI-SODIUM CITRATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.9→47.74 Å / Num. obs: 30076 / % possible obs: 99.3 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PT6

1pt6


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.735 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22884 1502 5 %RANDOM
Rwork0.18355 ---
obs0.18583 28552 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.55 Å20 Å2
2--1.09 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 2 184 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222992
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9514036
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65624.928138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91815550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7681518
X-RAY DIFFRACTIONr_chiral_restr0.1060.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022202
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8071.51872
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.81223028
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.13431120
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4514.51008
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 110 -
Rwork0.246 2099 -
obs--100 %

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