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- PDB-2jt9: NMR structure of immunosuppressory peptide containing cyclolinope... -

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Basic information

Entry
Database: PDB / ID: 2jt9
TitleNMR structure of immunosuppressory peptide containing cyclolinopeptide X and antennapedia(43-58) sequences
Components
  • 5-mer immunosuppressory peptide from cyclolinopeptide X
  • Modified 16-mer immunosuppressory peptide from Homeotic protein antennapedia
KeywordsIMMUNE SYSTEM / helix / cyclolinopeptide / immunosupression / ANTENNAPEDIA(43-58)
Function / homologyGAMMA-AMINO-BUTANOIC ACID / 6-AMINOHEXANOIC ACID
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsJaremko, L. / Jaremko, M. / Zhukov, I. / Cebrat, M.
CitationJournal: To be Published
Title: NMR structure of immunosuppressory peptide containing cyclolinopeptide X and antennapedia(43-58) sequences
Authors: Jaremko, L. / Jaremko, M. / Zhukov, I. / Cebrat, M. / Szewczuk, Z.
History
DepositionJul 21, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Atomic model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequences of the chain A and B are covalently linked by ACA-7. ABU-1 and NH2-24 are ...sequence The sequences of the chain A and B are covalently linked by ACA-7. ABU-1 and NH2-24 are covalently linked at the N-terminus of chain A and the C-terminus of chain B, respectively. The links between ACA/ABU/NH2 and other residues do not belong to regular peptide linking. The whole sequences represent immunosuppressory peptide containing cyclolinopeptide X and antennapedia. Chain B matches to the UniProtKB/Swiss-Prot entry P02833 homeotic protein antennapedia residues 339-354, with the following modifications:TRP-344 -> NAL, MET-350 -> NLE, TRP-352 -> NAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-mer immunosuppressory peptide from cyclolinopeptide X
B: Modified 16-mer immunosuppressory peptide from Homeotic protein antennapedia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0424
Polymers2,8082
Non-polymers2342
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 5-mer immunosuppressory peptide from cyclolinopeptide X


Mass: 551.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase peptide synthesis, FMOC strategy
#2: Protein/peptide Modified 16-mer immunosuppressory peptide from Homeotic protein antennapedia


Mass: 2255.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase peptide synthesis, FMOC strategy
#3: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Comment: inhibitor*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-1H TOCSY
1312D 1H-1H ROESY

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Sample preparation

DetailsContents: 2.5 mM polypeptide, methanol / Solvent system: methanol
SampleConc.: 2.5 mM / Component: entity
Sample conditionsIonic strength: 0.15 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UnityPlus / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 19

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