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- PDB-1cw8: SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO (mA-R)REGRIGGC I... -

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Basic information

Entry
Database: PDB / ID: 1cw8
TitleSOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO (mA-R)REGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 6 STRUCTURES
ComponentsHISTONE H3
KeywordsDNA BINDING PROTEIN / PSEUDOMIMETIC / SYNTHETIC PEPTIDE / RETRO-INVERSO ANALOGUE / TR-NOE / ANTIGEN- ANTIBODY COMPLEX
Function / homologyMETHYLMALONIC ACID
Function and homology information
MethodSOLUTION NMR / Energy minimisation Molecular dynamics (Simulated Annealing)
AuthorsPhan Chan Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, T.
CitationJournal: Biochemistry / Year: 2001
Title: Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach.
Authors: Phan-Chan-Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T.
History
DepositionAug 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_comp_id / _struct_conn.ptnr1_auth_seq_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_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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9652
Polymers8471
Non-polymers1181
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 50structures with the lowest energy
RepresentativeModel #5lowest energy

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Components

#1: Protein/peptide HISTONE H3


Mass: 846.980 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN 130-135 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence CGG was added as a linker to the dextran matrix in Biacore experiments via the Cys thiol group. NH2-CO was added at the C-terminal ...Details: The peptide was chemically synthesized. The sequence CGG was added as a linker to the dextran matrix in Biacore experiments via the Cys thiol group. NH2-CO was added at the C-terminal extremity of the retro-inverso peptide in order to mimic the N-terminal of the parent peptide. All non glycine residues present a D-configuration except CYS. Two RI(mA) diastereisomers were obtained and couldn't be separated.
#2: Chemical ChemComp-DXX / METHYLMALONIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: COSY, TOCSY, NOESY
NMR detailsText: The peptide/mAb molar ratio was adjusted to 50/1(i.e. 5 mM of peptide and 0.1 mM of mAb)

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Sample preparation

DetailsContents: 5 mM peptide, 0.1 mM mAb; 100 mM phosphate buffer containning 0.02% sodium azide
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.1M phosphate / pH: 7 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.4Guntert, Wuthrichstructure solution
Discover3Molecular Simulations Inc., San Diego, CAstructure solution
Discover3Molecular Simulations Inc., San Diego, CArefinement
XwinNMR1.2Brukercollection
RefinementMethod: Energy minimisation Molecular dynamics (Simulated Annealing)
Software ordinal: 1
Details: The structures are based on a set of 35 to 60 backbone-backbone, backbone-side chain and side chain-side chain distance restraints. The phi angle for the non glycine D-residues was ...Details: The structures are based on a set of 35 to 60 backbone-backbone, backbone-side chain and side chain-side chain distance restraints. The phi angle for the non glycine D-residues was constrained between 0 and 175. A distance dependent dielectric constant equal to 4r was applied. The net electric charges were decreased, while those of the N and C terminal charged groups were neglected.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 6

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