4KZE - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN RNA APTAMER IN COMPLEX WITH FAB

Authors :   H. Huang, N. B. Suslov, N. Li, Y. Koldobskaya, P. A. Rice, J. A. Piccirill

Date :   29 May 13 (Deposition) - 18 Jun 14 (Release) - 30 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : H,L,R
Biol. Unit 1: H,L,R  (1x)
Biol. Unit 2: H,L  (1x)
Biol. Unit 3: R  (1x)
Biol. Unit 4: H (1x),L (1x),R (1x)

Keywords :   G-Quadruplex, Fluorescence, Fluorophore Binding, Immune System-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Huang, N. B. Suslov, N. S. Li, S. A. Shelke, M. E. Evans, Y. Koldobskaya, P. A. Rice, J. A. Piccirilli
A G-Quadruplex-Containing Rna Activates Fluorescence In A Gfp-Like Fluorophore.
Nat. Chem. Biol. V. 10 686 2014
PubMed-ID: 24952597 | Reference-DOI: 10.1038/NCHEMBIO.1561

Molecule 1 - BL3-6 FAB ANTIBODY, HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - BL3-6 FAB ANTIBODY, LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - RNA (84-MER)
	Chains	:	R
	Engineered	:	YES
	Other Details	:	SPINACH RNA APTAMER
	Synthetic	:	YES

		1	2	3
Asymmetric Unit	:	H	L	R
Biological Unit 1 (1x)	:	H	L	R
Biological Unit 2 (1x)	:	H	L
Biological Unit 3 (1x)	:			R
Biological Unit 4 (1x)	:	H (1x)	L (1x)	R (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
2	K	1	Ligand/Ion	POTASSIUM ION
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GTP	-1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	G R:22 , G R:23 , G R:27 , U R:29 , G R:54 , G R:57 , G R:59	BINDING SITE FOR RESIDUE K R 101
2	AC2	SOFTWARE	HOH R:244 , HOH R:246 , HOH R:248 , HOH R:249	BINDING SITE FOR RESIDUE MG R 102

Asymmetric Unit

No.	Residues
1	H:25	-	H:99
2	H:152	-	H:208
3	H:228	-	L:215
4	L:24	-	L:89
5	L:135	-	L:195

Asymmetric Unit

No.	Residues
1	Phe H:158	-	Pro H:159
2	Glu H:160	-	Pro H:161
3	Ser L:8	-	Pro L:9
4	Phe L:95	-	Pro L:96
5	Tyr L:141	-	Pro L:142

(no "SAP(SNP)/Variant" information available for 4KZE)

(no "PROSITE Motif" information available for 4KZE)

(no "Exon" information available for 4KZE)

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
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Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..hhhhhh....ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kze H   4 EVQLVESGGGLVQPGGSLRLSCAASGFYISYSSIHWVRQAPGKGLEWVASISPYSGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARQGYRRRSGRGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kze L   1 SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSFPSTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain R from PDB  Type:RNA  Length:84
                                                                                                                    
                 4kze R   1 gGACGCGACCGAAAUGGUGAAGGACGGGUCCAGUGCGAAACACGCACUGUUGAGUAGAGUGUGAGCUCCGUAACUGGUCGCGUC  84
                            |       10        20        30        40        50        60        70        80    
                            1-GTP

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	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 4KZE)

(no "CATH Domain" information available for 4KZE)

(no "Pfam Domain" information available for 4KZE)

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		Phe H:158 - Pro H:159	[ RasMol ]
		Phe L:95 - Pro L:96	[ RasMol ]
		Ser L:8 - Pro L:9	[ RasMol ]
		Tyr L:141 - Pro L:142	[ RasMol ]

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		Biological Unit 4	[ Jena3D ]

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	4kze
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3ivk	BL3-6 FAB ANTIBODY GRAFT
4kzd

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

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