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- PDB-5e6w: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-I... -

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Basic information

Entry
Database: PDB / ID: 5e6w
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 / cellular extravasation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / negative regulation of dopamine metabolic process / neutrophil migration ...integrin alphaX-beta2 complex / cellular extravasation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / negative regulation of dopamine metabolic process / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / phagocytosis, engulfment / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / Integrin cell surface interactions / endothelial cell migration / specific granule membrane / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / positive regulation of superoxide anion generation / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor internalization / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / integrin binding / cell-cell signaling / extracellular vesicle / regulation of cell shape / amyloid-beta binding / 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 / metal ion binding / membrane / 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 EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. ...Integrin beta-2 subunit / 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 / 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 domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Mar 15, 2017Group: Database references / Experimental preparation / Other
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 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 1.7Sep 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
Revision 1.8Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 0This entry 5E6W reflects an alternative modeling of the structural data in r2P28SF original data ...This entry 5E6W reflects an alternative modeling of the structural data in r2P28SF original data determined by Authors: 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

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Assembly

Deposited unit
A: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3413
Polymers34,8981
Non-polymers4422
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.260, 52.260, 423.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: 34898.453 Da / Num. of mol.: 1 / Fragment: UNP residues 23-122, 362-574
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural 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


Mass: 18.015 Da / Num. of mol.: 185 / 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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.7 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2P28

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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

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUK

1yuk


Resolution: 2.2→24.971 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 964 5.15 %Random selection
Rwork0.2274 ---
obs0.2295 18723 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→24.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 28 185 2567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042458
X-RAY DIFFRACTIONf_angle_d0.8563330
X-RAY DIFFRACTIONf_dihedral_angle_d14.7381529
X-RAY DIFFRACTIONf_chiral_restr0.048363
X-RAY DIFFRACTIONf_plane_restr0.004442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.3160.33821320.27842426X-RAY DIFFRACTION99
2.316-2.4610.33321460.26972450X-RAY DIFFRACTION100
2.461-2.65080.33921490.26142491X-RAY DIFFRACTION100
2.6508-2.91720.32171390.24982506X-RAY DIFFRACTION100
2.9172-3.33850.29141350.23522520X-RAY DIFFRACTION100
3.3385-4.20290.24491260.20262593X-RAY DIFFRACTION99
4.2029-24.97270.23121370.21792773X-RAY DIFFRACTION97
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)
12.4309-0.0981-1.30131.69921.67331.62650.06650.04350.01520.37410.0385-0.06470.5878-0.03460.05110.34980.0234-0.06270.1682-0.07380.2584-14.367320.036113.4712
21.56170.8064-1.1231.3591-0.98390.6630.2594-0.15970.0870.1559-0.0994-0.0241-0.22330.0898-0.09910.322-0.11210.00730.4059-0.08880.4899-19.031744.341667.4889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 460 )
2X-RAY DIFFRACTION2chain 'A' and (resid 461 through 556 )

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