1SI3 Gene Regulation Rna date Feb 27, 2004
title Crystal Structure Of The Paz Domain Of Human Eif2c1 In Complex With A 9-Mer Sirna-Like Duplex
authors K.Ye, J.B.Ma, D.Patel
compound source
Molecule: 5'-R(Cpgpupgpapcpupcpu)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Eukaryotic Translation Initiation Factor 2c 1
Chain: A
Fragment: Paz Domain (Residues 225-369)
Synonym: Eif2c 1, Eif-2c 1, Putative Rna-Binding Protein Q99, Argonaute1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eif2c1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19b
symmetry Space Group: P 64
R_factor 0.247 R_Free 0.304
length a length b length c angle alpha angle beta angle gamma
99.799 99.799 34.933 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand MSE enzyme
note 1SI3 (Molecule of the Month:pdb98)
related structures by homologous chain: 1R4K, 1SI2
Primary referenceStructural basis for overhang-specific small interfering RNA recognition by the PAZ domain., Ma JB, Ye K, Patel DJ, Nature 2004 May 20;429(6989):318-22. PMID:15152257
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (1si3.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 1SI3
  • CSU: Contacts of Structural Units for 1SI3
  • Likely Quarternary Molecular Structure file(s) for 1SI3
  • Structure Factors (66 Kb)
  • Retrieve 1SI3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SI3 from S2C, [Save to disk]
  • Re-refined 1si3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SI3 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 1SI3
  • 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 1SI3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1si3a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1si3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1si3_B] [1si3] [1si3_A]
  • SWISS-PROT database: [Q9UL18]
  • Domain organization of [AGO1_HUMAN] by SWISSPFAM
  • Domain found in 1SI3: [PAZ ] by SMART
  • Other resources with information on 1SI3
  • Community annotation for 1SI3 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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