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- PDB-1ct6: SOLUTION STRUCTURE OF CGGIRGERG IN CONTACT WITH THE MONOCLONAL AN... -

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Basic information

Entry
Database: PDB / ID: 1ct6
TitleSOLUTION STRUCTURE OF CGGIRGERG IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 11 STRUCTURES
ComponentsHISTONE H3 PEPTIDE
KeywordsDNA BINDING PROTEIN / SYNTHETIC PEPTIDE / ANALOGUE / TR-NOE / ANTIGEN-ANTIBODY COMPLEX
Function / homology
Function and homology information


chromatin organization => GO:0006325 / DNA replication-dependent chromatin assembly / nuclear chromosome / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression ...chromatin organization => GO:0006325 / DNA replication-dependent chromatin assembly / nuclear chromosome / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H3.1 / Histone H3.1
Similarity search - Component
MethodSOLUTION NMR / ENERGY MINIMISATION MOLECULAR DYNAMICS
AuthorsPhan Chan Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.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 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: HISTONE H3 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)9061
Polymers9061
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)11 / 50structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

#1: Protein/peptide HISTONE H3 PEPTIDE


Mass: 906.024 Da / Num. of mol.: 1 / Fragment: C-TERMINAL REGION 130-135 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THEC-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB4X11 MONOCLONAL ANTIBODY (IGG1). ...Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THEC-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB4X11 MONOCLONAL ANTIBODY (IGG1). THE SEQUENCE CGG WAS ADDED TO THE N- TERMINUS OF THE IRGERA SEQUENCE AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. ALA WAS REPLACED BY GLY.
References: UniProt: P16106, UniProt: P68431*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: TOCSY, NOESY, COSY
NMR detailsText: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5MM OF PEPTIDE AND 0.1 MM MAB)

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Sample preparation

DetailsContents: 5 MM PEPTIDE, 0.1 MM MAB; 100 MM PHOSPHTE BUFFER CONTAINING 0.02% SODIUM AZIDE
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.refinement
RefinementMethod: ENERGY MINIMISATION MOLECULAR DYNAMICS / Software ordinal: 1
Details: ENERGY MINIMISATION. A DISTANT 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 ...Details: ENERGY MINIMISATION. A DISTANT 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. IN THE PDB, NH3+ IS INCLUDED IN THE RESIDUE CYS, AND COO- IS INCLUDED IN THE RESIDUE GLY. THE RESIDUE GLU HAS MISSING ATOMS HE2 IN ALL STRUCTURES BECAUSE IN DISCOVER, THIS RESIDUE IS MODELLED AS A CHARGED GROUP(WE HAVE COO- AND NOT COOH).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 11

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