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- PDB-2p28: Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit -

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Basic information

Entry
Database: PDB / ID: 2p28
TitleStructure of the PHE2 and PHE3 fragments of the integrin beta2 subunit
Components(Integrin beta-2) x 2
KeywordsCELL ADHESION / integrin beta2 subunit / hybrid domain / PSI domain / I-EGF domains
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 / receptor clustering / amyloid-beta clearance / 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 / heat shock protein binding / cell adhesion molecule 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
N-terminal domain of TfIIb - #10 / Integrin beta-2 subunit / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / N-terminal domain of TfIIb / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain ...N-terminal domain of TfIIb - #10 / Integrin beta-2 subunit / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / N-terminal domain of TfIIb / 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 / Other non-globular / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Special / Ribbon / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShi, M. / Foo, S.Y. / Tan, S.M. / Mitchell, E.P. / Law, S.K.A. / Lescar, J.
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.A. / Lescar, J.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-2
B: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1383
Polymers34,9172
Non-polymers2211
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-22 kcal/mol
Surface area18450 Å2
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 ...Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta / CD18 antigen


Mass: 11037.438 Da / Num. of mol.: 1 / Fragment: PHE2 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pIRES2-EGFP / Cell line (production host): HEK293_Gnti / Production host: Homo sapiens (human) / References: UniProt: P05107
#2: Protein Integrin beta-2 / Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 subunit beta / Complement receptor C3 ...Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta / CD18 antigen


Mass: 23879.072 Da / Num. of mol.: 1 / Fragment: PHE3 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pIRES2-EGFP / Cell line (production host): HEK293_Gnti / Production host: Homo sapiens (human) / References: UniProt: P05107
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulphate, 15% PEG4000, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 18866
Reflection shellResolution: 2.2→2.257 Å

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Processing

Software
NameVersionClassificationNB
AMoREphasing
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUK, 1L3Y

1yuk

1l3y


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.734 / SU ML: 0.196 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.308 964 5.1 %RANDOM
Rwork0.261 ---
obs0.263 18723 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 15 199 2569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212408
X-RAY DIFFRACTIONr_bond_other_d0.0020.022053
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9633257
X-RAY DIFFRACTIONr_angle_other_deg0.834816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125305
X-RAY DIFFRACTIONr_chiral_restr0.0710.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022710
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
X-RAY DIFFRACTIONr_nbd_refined0.1740.2442
X-RAY DIFFRACTIONr_nbd_other0.2210.22404
X-RAY DIFFRACTIONr_nbtor_other0.0810.21536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.219
X-RAY DIFFRACTIONr_mcbond_it0.7161.51532
X-RAY DIFFRACTIONr_mcangle_it1.33722453
X-RAY DIFFRACTIONr_scbond_it1.3323876
X-RAY DIFFRACTIONr_scangle_it2.2814.5804
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.405 70
Rwork0.302 1255
obs-1325
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)
11.1953-0.3745-0.52420.62940.95192.0810.03570.1246-0.04280.17410.0322-0.06640.3092-0.1245-0.06790.50060.0153-0.05050.4081-0.06090.4655-13.571919.7659.1114
213.9432-6.6546-12.2916.784311.491528.27860.2904-0.19260.7016-0.1336-0.88470.30851.7915-0.78040.59430.7003-0.30670.01320.2709-0.21750.3286-21.935423.416742.1519
31.7190.7188-1.62890.59530.37033.96960.2513-0.06340.01950.083-0.1227-0.0328-0.22040.2268-0.12860.4187-0.08470.010.4547-0.06960.523-18.169544.74869.1864
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A - BA - B1 - 4311 - 92
22BB435 - 46696 - 127
33BB470 - 556131 - 217

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