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- PDB-1yuk: The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment fr... -

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Basic information

Entry
Database: PDB / ID: 1yuk
TitleThe crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution
Components
  • Integrin beta-2 A chain
  • Integrin beta-2 B chain
KeywordsCELL ADHESION / Integrin beta2 / hybrid domain / PSI domain / I-EGF domain / crystal structure of PSI/HYBRID/I-EGF1
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 / Toll Like Receptor 4 (TLR4) Cascade ...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 / Toll Like Receptor 4 (TLR4) Cascade / neutrophil migration / leukocyte migration involved in inflammatory response / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / 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
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 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) / Other non-globular / 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 1. / EGF-like domain signature 2. / Special / Ribbon / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Integrin beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsShi, M. / Sundramurthy, K. / Liu, B. / Tan, S.M. / Law, S.K. / Lescar, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin {beta}2 Subunit at 1.8-A Resolution
Authors: Shi, M. / Sundramurthy, K. / Liu, B. / Tan, S.M. / Law, S.K. / Lescar, J.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 A chain
B: Integrin beta-2 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3134
Polymers24,8702
Non-polymers4422
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-19 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.600, 31.818, 74.950
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integrin beta-2 A chain / Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 beta-subunit / CD18 / Complement receptor ...Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 beta-subunit / CD18 / Complement receptor C3 beta- subunit


Mass: 11386.844 Da / Num. of mol.: 1 / Fragment: PSI domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05107
#2: Protein Integrin beta-2 B chain / Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 beta-subunit / CD18 / Complement receptor ...Cell surface adhesion glycoproteins LFA- 1/CR3/p150 / 95 beta-subunit / CD18 / Complement receptor C3 beta- subunit


Mass: 13483.287 Da / Num. of mol.: 1 / Fragment: I-EGF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05107
#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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 / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.2M calcium acetate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97600, 1.5418
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
21.54181
ReflectionResolution: 1.8→8 Å / Num. obs: 37606 / % possible obs: 92.5 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.18

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→6 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 2 / σ(F): 441
RfactorNum. reflection% reflection
Rfree0.253 1233 4.9 %
Rwork0.234 --
obs0.234 -97.7 %
all-24802 -
Displacement parametersBiso mean: 69.99 Å2
Baniso -1Baniso -2Baniso -3
1-8.337 Å20 Å21.547 Å2
2---2.82 Å20 Å2
3----5.517 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 30 219 1906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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