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- PDB-5e6x: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-I... -

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Basic information

Entry
Database: PDB / ID: 5e6x
TitleRe-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit
ComponentsIntegrin beta-2
KeywordsCELL ADHESION / CD18 fragment
Function / homology
Function and homology information


integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process ...integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / phagocytosis, engulfment / amyloid-beta clearance / receptor clustering / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / cell adhesion molecule binding / heat shock protein binding / receptor-mediated endocytosis / neutrophil chemotaxis / cell-matrix adhesion / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / receptor internalization / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular vesicle / integrin binding / cell-cell signaling / amyloid-beta binding / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / 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-2 subunit / 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 domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSpringer, T.A. / Sen, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI CA031798 United States
CitationJournal: J. Biol. Chem. / Year: 2007
Title: A structural hypothesis for the transition between bent and extended conformations of the leukocyte beta2 integrins.
Authors: Shi, M. / Foo, S.Y. / Tan, S.M. / Mitchell, E.P. / Law, S.K. / Lescar, J.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Mar 15, 2017Group: Database references / Experimental preparation / Other
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.8Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0This entry 5E6X reflects an alternative modeling of the structural data in r2P26SF original data ...This entry 5E6X reflects an alternative modeling of the structural data in r2P26SF original data determined by Author:Shi, M., Foo, S.Y., Tan, S.M., Mitchell, E.P., Law, S.K.A., Lescar, J.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7244
Polymers31,0601
Non-polymers6643
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.489, 30.853, 65.157
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 31060.072 Da / Num. of mol.: 1 / Fragment: UNP residues 23-122 and 362 535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Production host: Homo sapiens (human) / References: UniProt: P05107
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.83 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2P26

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PHENIX / Version: 1.8.2_1309 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUK

1yuk


Resolution: 1.75→27.87 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 1116 5.12 %Random selection
Rwork0.1966 ---
obs0.1994 21812 91.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 42 260 2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032320
X-RAY DIFFRACTIONf_angle_d0.7253129
X-RAY DIFFRACTIONf_dihedral_angle_d11.524876
X-RAY DIFFRACTIONf_chiral_restr0.052343
X-RAY DIFFRACTIONf_plane_restr0.002422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.82970.4404620.32881520X-RAY DIFFRACTION53
1.8297-1.92610.33671100.27052168X-RAY DIFFRACTION78
1.9261-2.04680.26821410.22532792X-RAY DIFFRACTION99
2.0468-2.20480.26521440.21942820X-RAY DIFFRACTION100
2.2048-2.42650.22461540.21142813X-RAY DIFFRACTION100
2.4265-2.77740.26351610.21762816X-RAY DIFFRACTION100
2.7774-3.49810.25911640.18812844X-RAY DIFFRACTION100
3.4981-27.87370.21291800.16272923X-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)
10.91060.2806-0.37681.0506-0.22560.50250.0321-0.0132-0.08610.03940.03860.0097-0.0761-0.11350.00010.12920.01230.00460.10570.00790.1421-19.9977-7.3953-32.8185
20.30020.2544-0.07880.31710.19260.55010.2592-0.0904-0.3310.045-0.0644-0.15370.33040.18090.00290.2074-0.0032-0.06430.19130.02940.26835.1629-16.1358-15.7239
30.5763-0.3507-0.2270.5885-0.1570.30340.0389-0.2546-0.10430.31050.04450.1451-0.0610.2203-0.01990.1758-0.029-0.03010.1646-0.00180.12166.02-8.7908-11.1255
41.2849-0.1270.08560.336-0.33430.3646-0.0068-0.1980.15650.08330.06230.0185-0.15950.06670.00010.1704-0.00950.01470.1997-0.03110.16696.7744-3.7199-11.7936
50.0858-0.0033-0.00280.04420.00240.24840.0873-0.1696-0.06790.0854-0.018-0.18560.2810.0765-0.0020.2493-0.0103-0.00130.1962-0.01950.2679-11.7849-19.7209-39.5005
60.9452-0.03730.25870.32680.27910.32830.2810.0308-0.015-0.0835-0.0997-0.0334-0.2023-0.09420.15810.19330.07650.03050.16260.01220.1235-21.3802-11.5783-53.9363
70.5541-0.17650.06010.50870.22110.410.11930.28210.12010.0730.01680.0064-0.11020.02280.00350.21520.04450.01510.26740.05840.1701-35.3296-2.7556-47.5593
81.3167-0.15730.61981.92550.57940.51370.37570.5553-0.4142-0.0309-0.33240.25890.4450.14290.03950.26180.0679-0.04250.25590.01170.1841-44.4822-2.1595-44.5483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 344 )
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 435 )
6X-RAY DIFFRACTION6chain 'A' and (resid 436 through 473 )
7X-RAY DIFFRACTION7chain 'A' and (resid 474 through 505 )
8X-RAY DIFFRACTION8chain 'A' and (resid 506 through 519 )

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