5G4U - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   ASSOCIATION OF THREE TWO-K-TURN UNITS BASED ON KT-7 3BU,3NU, FORMING A TRIANGULAR-SHAPED STRUCTURE

Authors :   L. Huang, D. M. J. Lilley

Date :   17 May 16 (Deposition) - 28 Sep 16 (Release) - 28 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: E,F,G,H  (1x)
Biol. Unit 2: I,J,K,L  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Rna-Protein Complex, Rna, Kink Turn, L7Ae, Nano Crystal Packing, Nanotechnology (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Huang, D. M. J. Lilley
A Quasi-Cyclic Rna Nano-Scale Molecular Object Constructed Using Kink Turns.
Nanoscale V. 8 15189 2016
PubMed-ID: 27506301 | Reference-DOI: 10.1039/C6NR05186C

Molecule 1 - HMKT-7
	Chains	:	A, B, E, F, I, J
	Fragment	:	KINK TURN MOTIF
	Organism Scientific	:	HALOARCULA MARISMORTUI
	Organism Taxid	:	2238
	Synthetic	:	YES

Molecule 2 - 50S RIBOSOMAL PROTEIN L7AE
	Chains	:	C, D, G, H, K, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD PLYSS
	Fragment	:	K-TURN BINDING DOMAIN, RESIDUES 2-119
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	RIBOSOMAL PROTEIN L8E

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:					E	F	G	H
Biological Unit 2 (1x)	:									I	J	K	L
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 5G4U)

(no "Site" information available for 5G4U)

(no "SS Bond" information available for 5G4U)

Asymmetric Unit

No.	Residues
1	Asp C:54	-	Pro C:55
2	Asp D:54	-	Pro D:55
3	Asp G:54	-	Pro G:55
4	Asp H:54	-	Pro H:55
5	Asp K:54	-	Pro K:55
6	Asp L:54	-	Pro L:55

(no "SAP(SNP)/Variant" information available for 5G4U)

(no "PROSITE Motif" information available for 5G4U)

(no "Exon" information available for 5G4U)

Asymmetric 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:19
                                                   
                 5g4u A   1 GGCGAAGAUCCGGUGAGCC  19
                                    10

Chain B from PDB  Type:RNA  Length:19
                                                   
                 5g4u B   1 GGCGAAGAUCCGGUGAGCC  19
                                    10

Chain C from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhheeeehhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeee.hhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 5g4u C  -1 EASYVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQ 118
                                     8        18        28        38        48        58        68        78        88        98       108       118

Chain D from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh.eeee.hhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4u D   1 SYVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain E from PDB  Type:RNA  Length:19
                                                   
                 5g4u E   1 GGCGAAGAUCCGGUGAGCC  19
                                    10

Chain F from PDB  Type:RNA  Length:19
                                                   
                 5g4u F   1 GGCGAAGAUCCGGUGAGCC  19
                                    10

Chain G from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....eeeehhhhhhhhhhh....eeee.....hhhhh.hhhhhhhhh...eee..hhhhhhhhhh......eeeeee......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4u G   1 SYVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain H from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....eeeehhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeee.hhhhhhhhh.......eeeeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4u H   1 SYVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain I from PDB  Type:RNA  Length:19
                                                   
                 5g4u I   1 GGCGAAGAUCCGGUGAGCC  19
                                    10

Chain J from PDB  Type:RNA  Length:19
                                                   
                 5g4u J   1 GGCGAAGAUCCGGUGAGCC  19
                                    10

Chain K from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhh....eeeee....hhhhh.hhhhhhhhh...eeee.hhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4u K  -1 EASYVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQK 119
                                     8        18        28        38        48        58        68        78        88        98       108       118

Chain L from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeee.hhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4u L   1 SYVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQK 119
                                    10        20        30        40        50        60        70        80        90       100       110

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 '\|'

(no "SCOP Domain" information available for 5G4U)

(no "CATH Domain" information available for 5G4U)

(no "Pfam Domain" information available for 5G4U)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5g4u)

	Sites
(no "Sites" information available for 5g4u)

	Cis Peptide Bonds
		Asp C:54 - Pro C:55	[ RasMol ]
		Asp D:54 - Pro D:55	[ RasMol ]
		Asp G:54 - Pro G:55	[ RasMol ]
		Asp H:54 - Pro H:55	[ RasMol ]
		Asp K:54 - Pro K:55	[ RasMol ]
		Asp L:54 - Pro L:55	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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5g4t	THE STRUCTURE OF A QUASI-CYCLIC SIX K-TURN DUPLEX RNA SPECIES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (14, 14)

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