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- PDB-6ckb: Crystal structure of an extended beta3 integrin P33 -

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Basic information

Entry
Database: PDB / ID: 6ckb
TitleCrystal structure of an extended beta3 integrin P33
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 / integrin alphaIIb-beta3 complex ...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 / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / 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 / : / 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 / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / 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 / wound healing, spreading of epidermal cells / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / heterotypic cell-cell adhesion / 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 / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / receptor clustering / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / 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 / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation
Similarity search - Function
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 ...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 / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / 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 domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / 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. / Rossmann fold / 3-Layer(aba) Sandwich / 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: 2.8 Å
AuthorsZhou, D. / Zhu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL131386 United States
CitationJournal: Blood / Year: 2018
Title: Structure of an extended beta3integrin.
Authors: Zhou, D. / Thinn, A.M.M. / Zhao, Y. / Wang, Z. / Zhu, J.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 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_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_asym_id / _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_asym_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 23, 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
B: Chimera protein of Integrin beta-3 and Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0769
Polymers103,9052
Non-polymers1,1707
Water724
1
A: Chimera protein of Integrin beta-3 and Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4194
Polymers51,9531
Non-polymers4673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chimera protein of Integrin beta-3 and Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6565
Polymers51,9531
Non-polymers7044
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.080, 80.910, 126.720
Angle α, β, γ (deg.)90.00, 96.36, 90.00
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: 51952.691 Da / Num. of mol.: 2
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.: 1 / 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.: 5 / 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 20% PEG 6000, 0.1 M Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 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: 2.8→58.7 Å / Num. obs: 29474 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.89 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→58.7 Å / SU ML: 0.81 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.02
RfactorNum. reflection% reflection
Rfree0.2964 1479 5.03 %
Rwork0.2393 --
obs0.2422 29394 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→58.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7223 0 72 4 7299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097467
X-RAY DIFFRACTIONf_angle_d1.05210088
X-RAY DIFFRACTIONf_dihedral_angle_d18.4594639
X-RAY DIFFRACTIONf_chiral_restr0.0711120
X-RAY DIFFRACTIONf_plane_restr0.0051324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.43911550.4122456X-RAY DIFFRACTION98
2.8904-2.99370.49991380.45782508X-RAY DIFFRACTION99
2.9937-3.11350.5431250.46262563X-RAY DIFFRACTION100
3.1135-3.25520.43661540.38562503X-RAY DIFFRACTION100
3.2552-3.42680.36191080.32652532X-RAY DIFFRACTION100
3.4268-3.64150.40411190.31832553X-RAY DIFFRACTION100
3.6415-3.92260.33711310.26472515X-RAY DIFFRACTION100
3.9226-4.31730.28361350.21292555X-RAY DIFFRACTION100
4.3173-4.94170.25791450.17892555X-RAY DIFFRACTION100
4.9417-6.22490.2571490.21212549X-RAY DIFFRACTION100
6.2249-58.72930.22791200.18442626X-RAY DIFFRACTION100
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)
13.29984.5372-2.8266.8324-3.48357.44780.2551.81820.2967-0.52570.5195-2.1111-0.2171-0.5426-0.91061.51990.46460.45671.063-0.09761.6837-90.1262-102.9404130.3059
28.0393.9222.39272.31571.8180.0338-0.05-0.03450.73530.5055-0.14870.6877-0.18030.05370.16141.2002-0.25080.17960.86080.27341.0479-72.1739-77.0016148.9856
38.263-0.1983-2.66724.4161-1.17465.91320.3896-0.39190.31360.12260.0345-0.2438-1.34740.012-0.41341.0468-0.1603-0.04950.5846-0.06330.543-41.9721-69.1093155.743
45.85013.51342.99597.75572.92284.37220.50020.6291-0.20060.3209-0.1841-0.23440.51570.3728-0.17140.93610.10460.21770.82580.08260.9954-76.0846-90.9379143.4911
55.4075.69095.14566.04675.40284.845-0.28621.25950.7825-0.72511.4144-0.73180.14841.5133-0.40212.1895-0.21650.23141.2744-0.26751.6149-91.3674-127.4508119.7065
69.20160.6875-0.24182.7045-3.35714.31671.3643-0.93821.21311.6397-1.4610.9458-1.08860.10680.48261.8663-0.1496-0.01790.9774-0.25881.0246-92.5095-139.7817124.988
74.2377-0.86631.3182-0.0631-1.10861.70230.3640.6654-0.3363-0.1889-0.58710.00230.58860.55540.2770.88560.29-0.02920.981-0.28821.0029-57.0003-59.1799208.0241
84.56361.46461.4186.2875-1.95675.4746-0.28560.0049-0.4661-0.43550.0197-0.5094-0.97760.88910.30431.1066-0.1063-0.00621.6957-0.30690.7956-94.3795-50.9343188.7254
91.3948-1.68831.64867.8511-3.78356.4230.0333-0.0188-0.2545-0.6014-0.0060.36821.101-0.05110.0810.60960.01580.08490.9791-0.22420.8152-59.6925-64.8375211.8257
104.713-1.29920.81469.4427-3.41894.87741.15330.4646-0.7502-1.7183-0.51150.60351.02571.6088-0.66212.32660.0467-0.25181.0659-0.10851.0847-49.2457-75.3945245.0763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 409 )
5X-RAY DIFFRACTION5chain 'A' and (resid 410 through 439 )
6X-RAY DIFFRACTION6chain 'A' and (resid 440 through 464 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 125 )
8X-RAY DIFFRACTION8chain 'B' and (resid 126 through 281 )
9X-RAY DIFFRACTION9chain 'B' and (resid 282 through 420 )
10X-RAY DIFFRACTION10chain 'B' and (resid 421 through 465 )

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