4JRD - JenaLib

Title :   CRYSTAL STRUCTURE OF THE PARALLEL DOUBLE-STRANDED HELIX OF POLY(A) RNA

Authors :   N. Safaee, A. M. Noronha, G. Kozlov, D. Rodionov, C. J. Wilds, G. M. Sheld K. Gehring

Date :   21 Mar 13 (Deposition) - 05 Jun 13 (Release) - 12 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Parallel Double Helix, Poly(A), Mrna, Pabp, Poly(A) Motif, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Safaee, A. M. Noronha, D. Rodionov, G. Kozlov, C. J. Wilds, G. M. Sheldrick, K. Gehring
Structure Of The Parallel Duplex Of Poly(A) Rna: Evaluation Of A 50 Year-Old Prediction.
Angew. Chem. Int. Ed. Engl. V. 52 10370 2013
PubMed-ID: 23813654 | Reference-DOI: 10.1002/ANIE.201303461

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 18)

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A A:2 , A A:3 , A B:2	BINDING SITE FOR RESIDUE NH4 A 101
02	AC2	SOFTWARE	A A:3 , A A:4 , A A:11 , A B:3	BINDING SITE FOR RESIDUE NH4 A 102
03	AC3	SOFTWARE	A A:6 , A A:7 , HOH A:216 , A B:6	BINDING SITE FOR RESIDUE NH4 A 103
04	AC4	SOFTWARE	A A:5 , A A:9 , A A:10 , A B:9 , A B:10 , NH4 B:103	BINDING SITE FOR RESIDUE NH4 A 104
05	AC5	SOFTWARE	A A:4 , A A:10 , A A:11 , A B:10	BINDING SITE FOR RESIDUE NH4 A 105
06	AC6	SOFTWARE	A A:11	BINDING SITE FOR RESIDUE NH4 A 106
07	AC7	SOFTWARE	A A:7 , A A:8 , HOH A:213 , A B:7 , A B:8	BINDING SITE FOR RESIDUE NH4 A 107
08	AC8	SOFTWARE	A A:8 , A A:9 , HOH A:233 , A B:8 , A B:9	BINDING SITE FOR RESIDUE NH4 A 108
09	AC9	SOFTWARE	A A:4 , A A:5 , HOH A:234 , A B:4 , A B:5	BINDING SITE FOR RESIDUE NH4 A 109
10	BC1	SOFTWARE	A A:7 , A A:8 , HOH A:227 , A B:5 , A B:6	BINDING SITE FOR RESIDUE NH4 A 110
11	BC2	SOFTWARE	A A:10 , A A:11 , A B:8 , A B:9	BINDING SITE FOR RESIDUE NH4 A 111
12	BC3	SOFTWARE	A A:1 , A A:11 , A B:9 , A B:10	BINDING SITE FOR RESIDUE NH4 B 101
13	BC4	SOFTWARE	A A:3 , A A:4 , A B:1 , A B:2 , HOH B:201	BINDING SITE FOR RESIDUE NH4 B 102
14	BC5	SOFTWARE	A A:5 , A A:6 , A A:9 , NH4 A:104 , A B:5 , A B:6	BINDING SITE FOR RESIDUE NH4 B 103
15	BC6	SOFTWARE	A A:9 , A A:10 , A B:5 , A B:7 , A B:8 , HOH B:213	BINDING SITE FOR RESIDUE NH4 B 104
16	BC7	SOFTWARE	A A:4 , A A:5 , A B:2 , A B:3 , HOH B:204	BINDING SITE FOR RESIDUE NH4 B 105
17	BC8	SOFTWARE	A A:6 , A A:7 , A B:4 , A B:5 , HOH B:210	BINDING SITE FOR RESIDUE NH4 B 106
18	BC9	SOFTWARE	A A:5 , A A:6 , A B:3 , A B:4 , HOH B:214	BINDING SITE FOR RESIDUE NH4 B 107

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:RNA  Length:11
                                          
                  4jrd A  1 AAAAAAAAAAA 11
                                    10

Chain B from PDB  Type:RNA  Length:11
                                          
                  4jrd B  1 AAAAAAAAAAA 11
                                    10

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		NH4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jrd)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4jrd
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP \| HSSP
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

Description