3UF1 Structural Protein date Oct 31, 2011
title Crystal Structure Of Vimentin (Fragment 144-251) From Homo S Northeast Structural Genomics Consortium Target Hr4796b
authors A.Kuzin, M.Abashidze, S.M.Vorobiev, P.Patel, R.Xiao, C.Ciccosanti R.Shastry, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelion J.F.Hunt, Northeast Structural Genomics Consortium (Nesg)
compound source
Molecule: Vimentin
Chain: A, B, C, D
Fragment: Residues 144-255
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vim
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.017 86.810 114.927 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand MSE enzyme
note 3UF1 supersedes 3OL1
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceThe structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and X-ray crystallography., Aziz A, Hess JF, Budamagunta MS, Voss JC, Kuzin AP, Huang YJ, Xiao R, Montelione GT, FitzGerald PG, Hunt JF, J Biol Chem. 2012 Aug 17;287(34):28349-61. doi: 10.1074/jbc.M111.334011. Epub, 2012 Jun 26. PMID:22740688
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk]
  • Biological Unit Coordinates (3uf1.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (3uf1.pdb2.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 3UF1
  • CSU: Contacts of Structural Units for 3UF1
  • Structure Factors (221 Kb)
  • Retrieve 3UF1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UF1 from S2C, [Save to disk]
  • Re-refined 3uf1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UF1 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 3UF1
  • 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 3UF1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q3uf1, region F:20-129 [Jmol] [rasmolscript] [script source]
  • Fold representative 3uf1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3uf1_B] [3uf1_A] [3uf1] [3uf1_D] [3uf1_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3UF1
  • Community annotation for 3UF1 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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