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
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
  • Alignments of the sequence of 3UF1 with the sequences similar proteins can be viewed for 3UF1's classification 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 at ProtoMap. Click on the Cluster number.
  • 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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