3C2I Transcription Regulator date Jan 25, 2008
title The Crystal Structure Of Methyl-Cpg Binding Domain Of Human Mecp2 In Complex With A Methylated Dna Sequence From Bdnf
authors K.L.Ho, I.W.Mcnae, L.Schmiedeberg, R.J.Klose, A.P.Bird, M.D.Walkinshaw
compound source
Molecule: Methyl-Cpg-Binding Protein 2
Chain: A
Fragment: Unp Residues 77-167, Human Mecp2 Mbd Domain
Synonym: Mecp-2 Protein, Mecp2
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mecp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30b

Molecule: Dna (5'-D(Dtpdcpdtpdgpdgpdapdap(5cm) Pdgpdgpdapdapdtpdtpdcpdtpdtpdcpdtpda)-3');
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: Dna (5'- D(Dapdtpdapdgpdapdapdgpdapdapdtpdtpdcp(5cm) Pdgpdtpdtpdcpdcpdapdg)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligonucleotide
symmetry Space Group: C 1 2 1
R_factor 0.212 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.710 53.600 65.730 90.00 132.10 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 5CM, MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMeCP2 binding to DNA depends upon hydration at methyl-CpG., Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP, Walkinshaw MD, Mol Cell. 2008 Feb 29;29(4):525-31. PMID:18313390
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (3c2i.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3C2I
  • CSU: Contacts of Structural Units for 3C2I
  • Likely Quarternary Molecular Structure file(s) for 3C2I
  • Structure Factors (200 Kb)
  • Retrieve 3C2I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C2I from S2C, [Save to disk]
  • Re-refined 3c2i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C2I in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3C2I
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3C2I, from MSDmotif at EBI
  • Fold representative 3c2i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c2i_B] [3c2i] [3c2i_C] [3c2i_A]
  • SWISS-PROT database: [P51608]
  • Domain organization of [MECP2_HUMAN] by SWISSPFAM
  • Domain found in 3C2I: [MBD ] by SMART
  • Alignments of the sequence of 3C2I with the sequences similar proteins can be viewed for 3C2I's classification [MECP2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [MECP2_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3C2I
  • Community annotation for 3C2I at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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