3HAY	Isomerase Biosynthetic Protein Rna	date	May 03, 2009
title	Crystal Structure Of A Substrate-Bound Full Haca Rnp From P Furiosus
authors	K.Ye
compound		source
Molecule: Probable Trna Pseudouridine Synthase B Chain: A Synonym: Trna Pseudouridine 55 Synthase, Psi55 Synthase, Tr Isomerase, Trna Pseudouridylate Synthase; Ec: 5.4.99.- Engineered: Yes		Organism_scientific: Pyrococcus Furiosus Organism_taxid: 2261 Gene: Trub, Pf1785 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Small Nucleolar Rnp Gar1-Like Protein Chain: B Synonym: Gar1 Engineered: Yes		Organism_scientific: Pyrococcus Furiosus Organism_taxid: 2261 Gene: Pf1791 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ribosome Biogenesis Protein Nop10 Chain: C Engineered: Yes		Organism_scientific: Pyrococcus Furiosus Organism_taxid: 2261 Gene: Pf1141 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: 50s Ribosomal Protein L7ae Chain: D Engineered: Yes		Organism_scientific: Pyrococcus Furiosus Organism_taxid: 2261 Gene: Rpl7ae, Pf1367 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Haca Rna Chain: E Engineered: Yes		Synthetic: Yes Other_details: Rna Was Prepared By In Vitro Transcription
Molecule: 5'-R(Apupapapupup(Fhu)Pgpapcpupcpap Chain: F Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 64 2 2	R_factor 0.323 R_Free 0.367
crystal cell	length a length b length c angle alpha angle beta angle gamma 189.518 189.518 279.045 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	4.99 Å
ligand	FHU, ZN	enzyme	Isomerase E.C.5.4.99 BRENDA
Gene Ontology	Chain Function Process Component A B C D ribonuclease P activity
Primary reference	Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase., Duan J, Li L, Lu J, Wang W, Ye K, Mol Cell. 2009 May 14;34(4):427-39. PMID:19481523

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk] Biological Unit Coordinates (3hay.pdb1.gz) 123 Kb LPC: Ligand-Protein Contacts for 3HAY CSU: Contacts of Structural Units for 3HAY Likely Quarternary Molecular Structure file(s) for 3HAY Structure Factors (110 Kb) Retrieve 3HAY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3HAY from S2C, [Save to disk] Re-refined 3hay structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3HAY 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 3HAY

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 3D motif for 3HAY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3hay_C] [3hay_E] [3hay_D] [3hay] [3hay_A] [3hay_F] [3hay_B] SWISS-PROT database: [Q8U1R4] [Q8U029] [Q8U160] [Q7LWY0] Domain organization of [NOP10_PYRFU] [Q8U029_PYRFU] [RL7A_PYRFU] [TRUB_PYRFU] by SWISSPFAM Domains found in 3HAY: [DKCLD] [PUA ] by SMART

Other resources with information on 3HAY

Community annotation for 3HAY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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Images from IMB Jena Image Library of Biological Macromolecules.

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