[English] 日本語
Yorodumi- PDB-1cs9: SOLUTION STRUCTURE OF CGGIRGERA IN CONTACT WITH THE MONOCLONAL AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cs9 | ||||||
---|---|---|---|---|---|---|---|
Title | SOLUTION STRUCTURE OF CGGIRGERA IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES | ||||||
Components | HISTONE H3 PEPTIDE | ||||||
Keywords | DNA BINDING PROTEIN / SYNTHETIC PEPTIDE / 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 / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...chromatin organization => GO:0006325 / DNA replication-dependent chromatin assembly / nuclear chromosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Method | SOLUTION NMR / ENERGY MINIMIZATION MOLECULAR DYNAMICS | ||||||
Authors | Phan Chan Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1cs9.cif.gz | 20.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1cs9.ent.gz | 15.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cs9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/1cs9 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/1cs9 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 920.050 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 THE C-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB 4X11 MONOCLONAL ANTIBODY (IGG1). ...Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THE C-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB 4X11 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. References: UniProt: P16106, UniProt: P68431*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: TOCSY, NOESY, COSY |
NMR details | Text: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5MM OF PEPTIDE AND 0.1MM OF MAB) |
-Sample preparation
Details | Contents: 5 MM PEPTIDE, 0.1MM MAB; 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE |
---|---|
Sample conditions | Ionic strength: 0.1M PHOSPHATE / pH: 7 / Pressure: 1 atm / Temperature: 277 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 400 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: ENERGY MINIMIZATION 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 ALA. 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 representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 7 |