5FJ4 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS STEM LOOP BOUND WITH U1A AND L7AE PROTEINS

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

Date :   06 Oct 15 (Deposition) - 25 May 16 (Release) - 06 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Transcription, Kink Turn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Huang, J. Wang, D. M. J. Lilley
A Critical Base Pair In K-Turns Determines The Conformational Class Adopted, And Correlates With Biological Function.
Nucleic Acids Res. V. 44 5390 2016
PubMed-ID: 27016741 | Reference-DOI: 10.1093/NAR/GKW201

Molecule 1 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
	Chains	:	A, B, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD PLYSS
	Expression System Vector	:	PT7
	Expression System Vector Type	:	PLASMID
	Fragment	:	RRM 1 DOMAIN, UNP RESIDUES 1-102
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U1 SNRNP A, U1-A, U1A

Molecule 2 - HMKT-7
	Chains	:	D, H
	Fragment	:	KINK TURN MOTIF
	Organism Scientific	:	HALOARCULA MARISMORTUI
	Organism Taxid	:	2238
	Synthetic	:	YES

Molecule 3 - 50S RIBOSOMAL PROTEIN L7AE
	Atcc	:	49558
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD PLYSS
	Expression System Vector	:	PET-DUET1
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA BINDING DOMAIN, UNP RESIDUES 5-119
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	224325
	Strain	:	DSM 4304
	Synonym	:	RIBOSOMAL PROTEIN L8E, AFL7AE

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 5FJ4)

(no "Site" information available for 5FJ4)

(no "SS Bond" information available for 5FJ4)

Asymmetric Unit

No.	Residues
1	Gly A:99	-	Thr A:100
2	Arg B:47	-	Ser B:48
3	Thr B:100	-	Phe B:101
4	Ala C:0	-	Ser C:1
5	Gly E:99	-	Thr E:100
6	Arg F:47	-	Ser F:48
7	Ala G:0	-	Ser G:1

(no "SAP(SNP)/Variant" information available for 5FJ4)

(no "PROSITE Motif" information available for 5FJ4)

(no "Exon" information available for 5FJ4)

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:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeeee........eeeeee.hhhhhhhhhhhh..........eeee....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5fj4 A   6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102
                                    15        25        35        45        55        65        75        85        95

Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeeee........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee...hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5fj4 B   6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102
                                    15        25        35        45        55        65        75        85        95

Chain C from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh....eeehhhhhhhhhhh....eeeee.....hhhhhhhhhhhhh....eeee.hhhhhhhhhh......eeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5fj4 C   0 ASYVKFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGL 117
                                     9        19        29        39        49        59        69        79        89        99       109

Chain D from PDB  Type:RNA  Length:35
                                                                   
                 5fj4 D   1 GAGGGAGCGCCAUUGCACUCCGGUGCGAAGAACUC  35
                                    10        20        30

Chain E from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeeee.........eeeee.hhhhhhhhhhhh..........eeee....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5fj4 E   6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102
                                    15        25        35        45        55        65        75        85        95

Chain F from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeeee........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5fj4 F   6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102
                                    15        25        35        45        55        65        75        85        95

Chain G from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.....eeeehhhhhhhhhhh....eeeee....hhhhh.hhhhhhhhh...eeee.hhhhhhhhhh......eeeeee....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5fj4 G   0 ASYVKFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGL 117
                                     9        19        29        39        49        59        69        79        89        99       109

Chain H from PDB  Type:RNA  Length:35
                                                                   
                 5fj4 H   1 GAGGGAGCGCCAUUGCACUCCGGUGCGAAGAACUC  35
                                    10        20        30

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 5FJ4)

(no "CATH Domain" information available for 5FJ4)

(no "Pfam Domain" information available for 5FJ4)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 5fj4)

	Cis Peptide Bonds
		Ala C:0 - Ser C:1	[ RasMol ]
		Ala G:0 - Ser G:1	[ RasMol ]
		Arg B:47 - Ser B:48	[ RasMol ]
		Arg F:47 - Ser F:48	[ RasMol ]
		Gly A:99 - Thr A:100	[ RasMol ]
		Gly E:99 - Thr E:100	[ RasMol ]
		Thr B:100 - Phe B:101	[ RasMol ]

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

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5fj0	STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS SIMPLE DUPLEX IN P4222 SPACE GROUP
5fj1	STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS STEM LOOP IN P212121 SPACE GROUP
5fjc	SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT C-2BU

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

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Exons (0, 0)

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Gene Ontology (28, 31)

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