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- PDB-2p26: Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit -

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Basic information

Entry
Database: PDB / ID: 2p26
TitleStructure of the PHE2 and PHE3 fragments of the integrin beta2 subunit
ComponentsIntegrin beta-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 / 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 / receptor-mediated endocytosis / cell adhesion molecule binding / cell-matrix adhesion / neutrophil chemotaxis / 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 / extracellular vesicle / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / 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 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 / 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 / Laminin / Laminin / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Ribbon / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 6, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_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_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7244
Polymers31,0601
Non-polymers6643
Water4,828268
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 ...Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta / CD18 antigen


Mass: 31060.072 Da / Num. of mol.: 1 / Fragment: PHE2 and PHE3
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: 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.: 268 / 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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Magnesium acetate, 0.1M sodium acetate, pH4.6, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorDate: Aug 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→27.87 Å / Num. obs: 21822

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å27.87 Å
Translation2.5 Å27.87 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YUK

1yuk


Resolution: 1.75→27.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.87 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1117 5.1 %RANDOM
Rwork0.204 ---
obs0.207 21815 91.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.2 Å2
2---0.02 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 42 268 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212281
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9673095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74424.22109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7831518
X-RAY DIFFRACTIONr_chiral_restr0.080.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021740
X-RAY DIFFRACTIONr_nbd_refined0.1890.2957
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.2157
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.241
X-RAY DIFFRACTIONr_mcbond_it0.3781.51448
X-RAY DIFFRACTIONr_mcangle_it0.64922275
X-RAY DIFFRACTIONr_scbond_it1.1013907
X-RAY DIFFRACTIONr_scangle_it1.7944.5820
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.592 36 -
Rwork0.404 817 -
obs-853 48.41 %
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)
12.06580.1150.72792.2788-0.29211.72430.0247-0.04-0.05970.0526-0.00080.0902-0.0941-0.101-0.0240.06220.0117-0.00350.00560.00140.0181-18.898-7.859-32.05
27.8094-1.52932.8792.0915-2.51589.00430.591-0.0352-1.81470.0828-0.2474-0.19950.97721.0782-0.34360.30170.0437-0.07590.33940.10470.464312.032-18.827-11.832
33.9144-0.45090.94981.3659-0.04211.34440.0428-0.4148-0.14060.20240.05560.04130.0195-0.0226-0.09830.0689-0.0193-0.00960.0287-0.006-0.03977.676-7.756-11.073
43.2338-0.66921.30062.6518-1.55018.0144-0.0421-0.63350.25840.29090.23430.096-0.0785-0.2294-0.19210.0431-0.0103-0.00010.0937-0.0809-0.03375.149-2.346-5.144
53.6964-0.13521.52440.3879-0.01321.25950.03940.0895-0.06570.0496-0.03210.0536-0.00290.1464-0.00730.0586-0.0193-0.00660.0098-0.0060.00895.966-6.934-20.77
61.9944-1.891-0.05822.23120.57893.87420.09160.0142-0.0987-0.1132-0.08950.0570.2312-0.0664-0.00210.0737-0.0058-0.0172-0.0050.015-0.0001-16.342-20.196-45.973
76.5756-2.84820.88714.9567-0.55135.18110.18840.35080.412-0.1237-0.2035-0.1579-0.1364-0.04580.01510.05360.0378-0.00750.060.0282-0.0193-20.867-12.589-52.915
83.3571.21232.94536.2386-0.83593.20610.37350.38320.4884-1.18350.1059-0.4308-0.60540.6698-0.47930.26390.0120.09950.20030.06870.0157-29.184-0.722-57.038
93.1521-0.6472-2.98931.80161.17724.31390.13890.43670.061-0.1408-0.1960.19490.018-0.12870.05710.02730.067-0.03620.08240.01-0.0674-38.594-5.863-45.324
1010.132-6.2355-5.71868.27150.11957.5520.04680.427-0.25680.04070.21470.74620.346-0.5641-0.26140.019-0.0229-0.05060.05630.0044-0.0246-46.183-1.723-41.892
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 631 - 63
2264 - 7564 - 75
3376 - 35176 - 112
44352 - 388113 - 149
55389 - 426150 - 187
66427 - 447188 - 208
77448 - 461209 - 222
88462 - 484223 - 245
99485 - 511246 - 272
1010512 - 519273 - 280

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