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- PDB-1ci5: GLYCAN-FREE MUTANT ADHESION DOMAIN OF HUMAN CD58 (LFA-3) -

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Basic information

Entry
Database: PDB / ID: 1ci5
TitleGLYCAN-FREE MUTANT ADHESION DOMAIN OF HUMAN CD58 (LFA-3)
ComponentsPROTEIN (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3(CD58))
KeywordsIMMUNE SYSTEM / ADHESION GLYCOPROTEIN / IMMUNOGLOBULIN SUPERFAMILY V-SET DOMAIN / CELL SURFACE RECEPTOR
Function / homology
Function and homology information


heterotypic cell-cell adhesion / ficolin-1-rich granule membrane / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to type II interferon / cellular response to tumor necrosis factor / signaling receptor binding / Neutrophil degranulation ...heterotypic cell-cell adhesion / ficolin-1-rich granule membrane / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to type II interferon / cellular response to tumor necrosis factor / signaling receptor binding / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lymphocyte function-associated antigen 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsSun, Z.Y.J. / Dotsch, V. / Kim, M. / Li, J. / Reinherz, E.L. / Wagner, G.
CitationJournal: EMBO J. / Year: 1999
Title: Functional glycan-free adhesion domain of human cell surface receptor CD58: design, production and NMR studies.
Authors: Sun, Z.Y. / Dotsch, V. / Kim, M. / Li, J. / Reinherz, E.L. / Wagner, G.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3(CD58))


Theoretical massNumber of molelcules
Total (without water)11,0031
Polymers11,0031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25LEAST ENERGY FUNCTION
RepresentativeModel #3

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Components

#1: Protein PROTEIN (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3(CD58)) / 1DCD58-6M


Mass: 11003.180 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN / Mutation: F1S/V9K/V21Q/V58K/T85S/L93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CELL SURFACE / Plasmid: PET11A-1DCD58X6 / Species (production host): Escherichia coli / Gene (production host): 1DCD58X6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19256

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121NOESY-HSQC
131HNCA
141CBCA(CO)NH
151HBHA(CBCACO)NH
161(H)CCH-TOCSY
171HNHA
181HNHB
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED 1DCD58-6M.

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Sample preparation

DetailsContents: 10% D2O
Sample conditionsIonic strength: 10 mM NAPO4 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Varian INOVA500VarianINOVA5005002
Varian INOVA750VarianINOVA7507503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
XEASYstructure solution
X-PLORstructure solution
DIANAstructure solution
DYANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: NO NOE VIOLATION GREATER THAN 0.3 A, NO DIHEDRAL ANGLE VIOLATION GREATER THAN 5 DEGREE. AVERAGE BACKBONE ATOM (RESIDUE 3 - 95) RMSD TO MEAN STRUCTURE 0.37 A, AVERAGE HEAVY ATOM (RESIDUE 3 - ...Details: NO NOE VIOLATION GREATER THAN 0.3 A, NO DIHEDRAL ANGLE VIOLATION GREATER THAN 5 DEGREE. AVERAGE BACKBONE ATOM (RESIDUE 3 - 95) RMSD TO MEAN STRUCTURE 0.37 A, AVERAGE HEAVY ATOM (RESIDUE 3 - 95) RMSD TO MEAN STRUCTURE 0.93 A.
NMR ensembleConformer selection criteria: LEAST ENERGY FUNCTION / Conformers calculated total number: 25 / Conformers submitted total number: 20

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