[English] 日本語
Yorodumi
- PDB-6bxj: Structure of a single-chain beta3 integrin -

+
Open data


ID or keywords:

Loading...

-
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 / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / cell-substrate junction assembly / RUNX3 Regulates Immune Response and Cell Migration / mesodermal cell differentiation / angiogenesis involved in wound healing / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / positive regulation of cell adhesion mediated by integrin / integrin complex / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of cell-matrix adhesion / smooth muscle cell migration / microvillus membrane / leukocyte cell-cell adhesion / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / receptor clustering / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / activation of protein kinase activity / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / specific granule membrane / coreceptor activity / phagocytosis / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / positive regulation of endothelial cell migration / protein kinase C binding / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / Cell surface interactions at the vascular wall / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / wound healing / cell-cell adhesion / platelet aggregation / platelet 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 beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain ...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 beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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 2. / EGF-like domain signature 1.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more