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- PDB-1l2z: CD2BP2-GYF domain in complex with proline-rich CD2 tail segment p... -

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Basic information

Entry
Database: PDB / ID: 1l2z
TitleCD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide
Components
  • CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2
  • T-CELL SURFACE ANTIGEN CD2
KeywordsPEPTIDE BINDING/SIGNALING PROTEIN / GYF domain / protein-protein interaction / proline-rich peptide / CD2 / CD2BP2 / PEPTIDE BINDING-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / spliceosomal tri-snRNP complex assembly / U5 snRNP / ribonucleoprotein complex binding / T cell activation ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / spliceosomal tri-snRNP complex assembly / U5 snRNP / ribonucleoprotein complex binding / T cell activation / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / fibrillar center / cell-cell adhesion / : / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell-cell junction / signaling receptor activity / cell surface receptor signaling pathway / nuclear speck / external side of plasma membrane / signaling receptor binding / apoptotic process / Golgi apparatus / cell surface / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GYF domain / T-cell surface antigen CD2 / CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Immunoglobulin C2-set / Immunoglobulin C2-set domain ...GYF domain / T-cell surface antigen CD2 / CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Dna Ligase; domain 1 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CD2 antigen cytoplasmic tail-binding protein 2 / T-cell surface antigen CD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFreund, C. / Kuhne, R. / Yang, H. / Park, S. / Reinherz, E.L. / Wagner, G.
CitationJournal: Embo J. / Year: 2002
Title: Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules
Authors: Freund, C. / Kuhne, R. / Yang, H. / Park, S. / Reinherz, E.L. / Wagner, G.
History
DepositionFeb 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2
B: T-CELL SURFACE ANTIGEN CD2


Theoretical massNumber of molelcules
Total (without water)8,5602
Polymers8,5602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2


Mass: 7320.014 Da / Num. of mol.: 1 / Fragment: Residue 1-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD2BP2 (amino acids 280-341) / Plasmid: PTFT74 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95400
#2: Protein/peptide T-CELL SURFACE ANTIGEN CD2 / T-cell surface antigen T11/Leu-5 / LFA-2 / LFA-3 receptor / Erythrocyte receptor / Rosette receptor


Mass: 1240.416 Da / Num. of mol.: 1 / Fragment: Residue 63-73 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P06729

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
1312D TOCSY
1413D 15N edited TOCSY
15115N HSQC
2622D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM GYF domain U-deuterated, U-15N, 1mM Peptide, 50 mM phosphate buffer, pH 6.3, 100% D2O100% D2O
21 mM GYF domain, aromatic amino acids protonated only, 1 mM Peptide protonated100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaPo4 6.3 1 atm298 K
250 mM NaPo4 6.3 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian UNITYVarianUNITY7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brunger, A.refinement
XEASYdata analysis
PROSAprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1000K, force constant NOE 50 kcal mol-1A-2, force constant dihedral angles 200 kcal mol-1 rad-2, 1000 steps minimization, intermolecular NOEs 33, intramolecular NOEs (peptide) 49, ...Details: 1000K, force constant NOE 50 kcal mol-1A-2, force constant dihedral angles 200 kcal mol-1 rad-2, 1000 steps minimization, intermolecular NOEs 33, intramolecular NOEs (peptide) 49, intramolecular NOEs (GYF domain) 754
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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