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- PDB-6bxj: Structure of a single-chain beta3 integrin -

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Basic information

Entry
Database: PDB / ID: 6bxj
TitleStructure of a single-chain beta3 integrin
ComponentsChimera protein of Integrin beta-3 and Integrin alpha-L
KeywordsCELL ADHESION / integrin
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / tube development / : / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / tube development / : / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / RUNX3 Regulates Immune Response and Cell Migration / positive regulation of vascular endothelial growth factor signaling pathway / glycinergic synapse / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / positive regulation of smooth muscle cell migration / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cellular response to insulin-like growth factor stimulus / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / microvillus membrane / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / receptor clustering / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / positive regulation of bone resorption / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / phagocytosis / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / specific granule membrane / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / protein kinase C binding / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / positive regulation of smooth muscle cell proliferation / regulation of actin cytoskeleton organization / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation
Similarity search - Function
Hormone receptor fold - #30 / Hormone receptor fold / 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 beta tail domain / Integrin EGF domain / Integrin beta subunit, tail ...Hormone receptor fold - #30 / Hormone receptor fold / 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 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 / 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 alpha, N-terminal / Integrin domain superfamily / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Ribbon / Few Secondary Structures / Irregular / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsThinn, A.M.M. / Wang, Z. / Zhou, D. / Zhao, Y. / Curtis, B.R. / Zhu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL131836 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122985 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Autonomous conformational regulation of beta3integrin and the conformation-dependent property of HPA-1a alloantibodies.
Authors: Thinn, A.M.M. / Wang, Z. / Zhou, D. / Zhao, Y. / Curtis, B.R. / Zhu, J.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Structure summary
Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of Integrin beta-3 and Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4487
Polymers69,5141
Non-polymers9336
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.460, 125.290, 70.020
Angle α, β, γ (deg.)90.000, 112.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chimera protein of Integrin beta-3 and Integrin alpha-L / Platelet membrane glycoprotein IIIa / GPIIIa / CD11 antigen-like family member A / Leukocyte ...Platelet membrane glycoprotein IIIa / GPIIIa / CD11 antigen-like family member A / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain


Mass: 69514.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A, ITGAL, CD11A / Production host: Homo sapiens (human) / References: UniProt: P05106, UniProt: P20701
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 4 / 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.: 596 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 8000, 20% 1,5-pentanediol, 4 mM alkalis, 66 mM Gly-Gly, 33 mM AMPD, pH 8.5.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.09→64 Å / Num. obs: 50880 / % possible obs: 98 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.23 Å2 / Net I/σ(I): 9
Reflection shellResolution: 2.09→2.15 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.092→47.292 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2343 2556 5.03 %
Rwork0.1864 --
obs0.1889 50811 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.92 Å2 / Biso mean: 57.4631 Å2 / Biso min: 18.82 Å2
Refinement stepCycle: final / Resolution: 2.092→47.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 58 596 5429
Biso mean--55.22 51.31 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024958
X-RAY DIFFRACTIONf_angle_d0.5516710
X-RAY DIFFRACTIONf_chiral_restr0.044738
X-RAY DIFFRACTIONf_plane_restr0.003880
X-RAY DIFFRACTIONf_dihedral_angle_d14.9283098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.092-2.13220.34051270.3232576270393
2.1322-2.17580.36981300.30492613274396
2.1758-2.22310.37461310.29392647277896
2.2231-2.27480.3551220.28692684280697
2.2748-2.33170.31291320.26572679281198
2.3317-2.39470.31511360.24122668280497
2.3947-2.46520.29581480.22372617276598
2.4652-2.54470.26571320.21032716284898
2.5447-2.63570.25111610.20972677283898
2.6357-2.74120.24081520.20582646279898
2.7412-2.86590.26291370.18932702283998
2.8659-3.0170.26491340.18962699283399
3.017-3.2060.25111380.18612732287099
3.206-3.45350.25571310.17822707283899
3.4535-3.80090.21411470.15892712285999
3.8009-4.35050.17481640.14732715287999
4.3505-5.47990.1731710.13492717288899
5.4799-47.30420.20721630.16372748291199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2039-0.08921.08720.0069-0.08180.9807-0.05670.10390.43440.02930.6473-1.2693-0.49271.38320.32620.7136-0.1668-0.28351.0146-0.49731.618650.586136.23685.6662
24.5062-2.6858-0.49793.1301-3.48169.3979-0.04720.3041-1.1229-0.02940.0498-0.22470.7258-0.3888-0.21520.23130.01560.02010.3308-0.06120.69131.36793.396668.8311
35.642.86340.672.80820.38930.4459-0.1742-0.01310.08330.06680.112-0.2652-0.02830.05990.01710.23440.0372-0.05350.23120.01320.385818.87219.238971.5587
43.6062-0.2278-0.17473.4912-0.1121.2792-0.0429-0.0451-0.0559-0.01580.07810.03290.03290.0046-0.0330.1707-0.01570.00310.1950.01210.28130.16850.244969.6828
55.63233.61742.90094.36672.05972.5057-0.0934-0.07750.01230.01870.0904-0.1647-0.0334-0.0314-0.06010.22180.0650.01150.2280.01250.339618.317615.067868.4262
67.52032.30352.20862.35481.07155.2898-0.399-0.76260.38690.4836-0.0044-0.4952-0.4835-0.11130.31580.45630.1387-0.17490.3408-0.0360.689233.160215.561483.1232
71.64940.35741.09020.11550.42861.67940.2493-0.3737-0.29160.2166-0.0236-0.17710.240.02610.73821.20560.0142-0.94321.2392-0.32991.659953.967336.5459105.655
86.67623.03884.27022.57353.70735.3442-0.44250.91093.14760.4936-0.0763-1.5387-2.77231.9440.52561.3512-0.3531-0.17041.03350.06551.449444.159757.804396.9907
92.53733.83921.88116.54121.147.47270.0505-0.10990.18670.67660.0906-0.8281-0.54020.5265-0.01530.7874-0.1061-0.22090.5599-0.01720.735335.591446.548599.1668
103.08860.5521.16448.64953.34892.8617-0.1438-0.44360.4110.367-0.41330.2558-0.8029-0.14840.54020.51970.017-0.06410.4752-0.08050.474122.156836.779282.0849
114.696-0.91132.93924.96250.14574.2347-0.05760.0757-0.2204-0.08730.0868-0.10990.080.0803-0.03180.238-0.020.0590.28630.00990.32743.649828.584853.5072
126.16181.13471.67446.84663.36247.8335-0.21360.6142-0.5774-0.6494-0.05760.36130.5857-0.14420.35010.4021-0.0524-0.05780.2926-0.04450.3587-6.383928.312144.0409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 59 )A1 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 86 )A60 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 125 )A87 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 271 )A126 - 271
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 348 )A272 - 348
6X-RAY DIFFRACTION6chain 'A' and (resid 349 through 377 )A349 - 377
7X-RAY DIFFRACTION7chain 'A' and (resid 378 through 413 )A378 - 413
8X-RAY DIFFRACTION8chain 'A' and (resid 420 through 430 )A420 - 430
9X-RAY DIFFRACTION9chain 'A' and (resid 431 through 465 )A431 - 465
10X-RAY DIFFRACTION10chain 'A' and (resid 466 through 501 )A466 - 501
11X-RAY DIFFRACTION11chain 'A' and (resid 502 through 588 )A502 - 588
12X-RAY DIFFRACTION12chain 'A' and (resid 589 through 625 )A589 - 625

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