4RBO Dna Binding Protein, Transcription Dna date Sep 12, 2014
title Crystal Structure Of A Nanog Homeobox (Nanog) From Homo Sapi 3.30 A Resolution
authors Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Stemcell)
compound source
Molecule: Putative Homeobox Protein Nanogp8
Chain: A, D
Fragment: Unp Residues 94-162
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nanogp8, Nm_024865
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: 46ektevlic

Molecule: 5'-D(Gpgpcpcpcpaptptpcpapapg)-3'
Chain: B, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Cptptpgpapaptpgpgpgpcpc)-3'
Chain: C, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 65 2 2
R_factor 0.235 R_Free 0.268
length a length b length c angle alpha angle beta angle gamma
215.603 215.603 42.269 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
Gene NM
A, D

Primary referenceStructure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells., Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ, Proc Natl Acad Sci U S A. 2015 Mar 30. pii: 201502855. PMID:25825768
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (4rbo.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (4rbo.pdb2.gz) 57 Kb
  • CSU: Contacts of Structural Units for 4RBO
  • Structure Factors (354 Kb)
  • Retrieve 4RBO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4RBO from S2C, [Save to disk]
  • Re-refined 4rbo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RBO 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 4RBO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4RBO, from MSDmotif at EBI
  • Fold representative 4rbo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rbo_C] [4rbo_A] [4rbo_E] [4rbo_B] [4rbo_F] [4rbo_D] [4rbo]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4RBO: [HOX ] by SMART
  • Other resources with information on 4RBO
  • Community annotation for 4RBO at PDBWiki (http://pdbwiki.org)

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