6BBO Hydrolase Rna date Oct 19, 2017
title Crystal Structure Of Human Apobec3hrna Complex
authors N.M.Shaban, K.Shi, S.Banerjee, R.S.Harris, H.Aihara
compound source
Molecule: Apobec3h
Chain: A, E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apobec3h
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'-R(Upapapapapapapa)-3')
Chain: B, F

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Rna (5'-R(Upupupupupupupu)-3')
Chain: C, G

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Mcherry Fluorescent Protein
Chain: D, H
Engineered: Yes

Organism_scientific: Discosoma Sp.
Organism_taxid: 86600
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 1 2
R_factor 0.364 R_Free 0.392
length a length b length c angle alpha angle beta angle gamma
101.293 101.293 211.217 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.43 Å
A, E
  • cytidine deaminase activity

  • H, D

    Primary referenceThe Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism., Shaban NM, Shi K, Lauer KV, Carpenter MA, Richards CM, Salamango D, Wang J, Lopresti MW, Banerjee S, Levin-Klein R, Brown WL, Aihara H, Harris RS, Mol Cell. 2018 Jan 4;69(1):75-86.e9. doi: 10.1016/j.molcel.2017.12.010. Epub 2017, Dec 28. PMID:29290613
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (312 Kb) [Save to disk]
  • Biological Unit Coordinates (6bbo.pdb1.gz) 157 Kb
  • Biological Unit Coordinates (6bbo.pdb2.gz) 159 Kb
  • CSU: Contacts of Structural Units for 6BBO
  • Structure Factors (594 Kb)
  • Retrieve 6BBO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6BBO from S2C, [Save to disk]
  • View 6BBO 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 6BBO
  • 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
  • Fold representative 6bbo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6bbo_B] [6bbo_G] [6bbo_E] [6bbo_C] [6bbo_A] [6bbo_D] [6bbo_H] [6bbo_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6BBO
  • Community annotation for 6BBO at PDBWiki (http://pdbwiki.org)

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