3RW6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF NUCLEAR RNA EXPORT FACTOR TAP BOUND TO CTE RNA

Authors :   M. Teplova, N. W. Khin, D. J. Patel, E. Izaurralde

Date :   07 May 11 (Deposition) - 10 Aug 11 (Release) - 02 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Retroviral Constitutive Transport Element (Cte), Rna Recognition Motif (Rrm), Leucine-Rich Repeat (Lrr) Motif, Transport Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Teplova, L. Wohlbold, N. W. Khin, E. Izaurralde, D. J. Patel
Structure-Function Studies Of Nucleocytoplasmic Transport O Retroviral Genomic Rna By Mrna Export Factor Tap.
Nat. Struct. Mol. Biol. V. 18 990 2011
PubMed-ID: 21822283 | Reference-DOI: 10.1038/NSMB.2094

Molecule 1 - NUCLEAR RNA EXPORT FACTOR 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	T7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 96-362
	Gene	:	NXF1, TAP, TAP (NXF1)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TIP-ASSOCIATED PROTEIN, TIP-ASSOCIATING PROTEIN, MRNA EXPORT FACTOR TAP

Molecule 2 - CONSTITUTIVE TRANSPORT ELEMENT(CTE)OF MASON-PFIZER MONKEY VIRUS RNA
	Chains	:	H, F
	Engineered	:	YES
	Other Details	:	ENZYMATIC SYNTHESIS
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	F	H
Biological Unit 1 (1x)	:	A			H
Biological Unit 2 (1x)	:		B	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CCC	2	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GTP	2	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CCC	1	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CCC	1	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE

(no "Site" information available for 3RW6)

(no "SS Bond" information available for 3RW6)

(no "Cis Peptide Bond" information available for 3RW6)

(no "SAP(SNP)/Variant" information available for 3RW6)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	NXF1_HUMAN	266-287 292-313 316-337	6	A:266-287 B:266-287 A:292-313 B:292-313 A:316-337 B:316-337

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	NXF1_HUMAN	266-287 292-313 316-337	3	A:266-287 - A:292-313 - A:316-337 -

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	NXF1_HUMAN	266-287 292-313 316-337	3	- B:266-287 - B:292-313 - B:316-337

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000294172	2b	ENSE00001198395	chr11:62572964-62572801	164	NXF1_HUMAN	1-10	10	0	-	-
1.4e	ENST00000294172	4e	ENSE00001063544	chr11:62571450-62571264	187	NXF1_HUMAN	10-72	63	0	-	-
1.4g	ENST00000294172	4g	ENSE00001198378	chr11:62571044-62570891	154	NXF1_HUMAN	72-123	52	2	A:118-123 B:117-123	6 7
1.5b	ENST00000294172	5b	ENSE00001198363	chr11:62569732-62569649	84	NXF1_HUMAN	124-151	28	2	A:124-151 B:124-151	28 28
1.6c	ENST00000294172	6c	ENSE00001198351	chr11:62569518-62569414	105	NXF1_HUMAN	152-186	35	2	A:152-186 B:152-186	35 35
1.7	ENST00000294172	7	ENSE00001198338	chr11:62569291-62569211	81	NXF1_HUMAN	187-213	27	2	A:187-213 B:187-213	27 27
1.8	ENST00000294172	8	ENSE00001198325	chr11:62569103-62569034	70	NXF1_HUMAN	214-237	24	2	A:214-237 B:214-237	24 24
1.9	ENST00000294172	9	ENSE00001198312	chr11:62568889-62568801	89	NXF1_HUMAN	237-266	30	2	A:237-266 B:237-266	30 30
1.10	ENST00000294172	10	ENSE00001198304	chr11:62568673-62568566	108	NXF1_HUMAN	267-302	36	2	A:267-302 B:267-302	36 36
1.11a	ENST00000294172	11a	ENSE00001198291	chr11:62567958-62567849	110	NXF1_HUMAN	303-339	37	2	A:303-339 B:303-339	37 37
1.11g	ENST00000294172	11g	ENSE00001198284	chr11:62566047-62566011	37	NXF1_HUMAN	339-351	13	2	A:339-351 B:339-351	13 13
1.12	ENST00000294172	12	ENSE00001063548	chr11:62564858-62564790	69	NXF1_HUMAN	352-374	23	2	A:352-362 B:352-360	11 9
1.13	ENST00000294172	13	ENSE00001063546	chr11:62564710-62564655	56	NXF1_HUMAN	375-393	19	0	-	-
1.15a	ENST00000294172	15a	ENSE00001063554	chr11:62564039-62563932	108	NXF1_HUMAN	393-429	37	0	-	-
1.16b	ENST00000294172	16b	ENSE00001141830	chr11:62563817-62563759	59	NXF1_HUMAN	429-449	21	0	-	-
1.17b	ENST00000294172	17b	ENSE00001141824	chr11:62563653-62563538	116	NXF1_HUMAN	449-487	39	0	-	-
1.18	ENST00000294172	18	ENSE00001141816	chr11:62563415-62563373	43	NXF1_HUMAN	488-502	15	0	-	-
1.19b	ENST00000294172	19b	ENSE00001274696	chr11:62562479-62562407	73	NXF1_HUMAN	502-526	25	0	-	-
1.20c	ENST00000294172	20c	ENSE00001063547	chr11:62561912-62561730	183	NXF1_HUMAN	526-587	62	0	-	-
1.21a	ENST00000294172	21a	ENSE00001764908	chr11:62560173-62560113	61	NXF1_HUMAN	587-607	21	0	-	-
1.21h	ENST00000294172	21h	ENSE00001198195	chr11:62559986-62559598	389	NXF1_HUMAN	608-619	12	0	-	-

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:245
 aligned with NXF1_HUMAN | Q9UBU9 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:245
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     
           NXF1_HUMAN   118 NWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKILDRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISAIRERFPKLLRLDGHELPPPIAF 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhhhhh.......eeeeee..eeeeee.hhhhhhhhhhh..............eeee...hhhhhh..hhhhhhhhhhhhhhhee....eee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhh....eee........hhhhhhhhhhh....eee.......hhhhhhhhh.....eee.....hhhhh.hhhhhhhhhhhhh....ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------LRR  PDB: A:266-287   ----LRR  PDB: A:292-313   --LRR  PDB: A:316-337   ------------------------- PROSITE
           Transcript 1 (1) 1.4g  Exon 1.5b  PDB: A:124-151   Exon 1.6c  PDB: A:152-186          Exon 1.7  PDB: A:187-213   Exon 1.8  PDB: A:214-237-----------------------------Exon 1.10  PDB: A:267-302           Exon 1.11a  PDB: A:303-339           ------------Exon 1.12   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:237-266      ------------------------------------------------------------------------Exon 1.11g   ----------- Transcript 1 (2)
                 3rw6 A 118 NWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKILDRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISAIRERFPKLLRLDGHELPPPIAF 362
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with NXF1_HUMAN | Q9UBU9 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:244
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356    
           NXF1_HUMAN   117 KNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKILDRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISAIRERFPKLLRLDGHELPPPI 360
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhh......eeeeee..eeeeee.hhhhhhhhhhh..............eeeee..hhhhhh..hhhhhhhhhhhhhhheehhh.eee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhh....eee........hhhhhhhhhhh....eee.......hhhhhhhh......eee.....hhhhh.hhhhhhhhhhh......ee..ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------LRR  PDB: B:266-287   ----LRR  PDB: B:292-313   --LRR  PDB: B:316-337   ----------------------- PROSITE
           Transcript 1 (1) 1.4g   Exon 1.5b  PDB: B:124-151   Exon 1.6c  PDB: B:152-186          Exon 1.7  PDB: B:187-213   Exon 1.8  PDB: B:214-237-----------------------------Exon 1.10  PDB: B:267-302           Exon 1.11a  PDB: B:303-339           ------------Exon 1.12 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:237-266      ------------------------------------------------------------------------Exon 1.11g   --------- Transcript 1 (2)
                 3rw6 B 117 KNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKILDRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISAIRERFPKLLRLDGHELPPPI 360
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356

Chain F from PDB  Type:RNA  Length:62
                                                                                              
                 3rw6 F   1 gGCACUAACCUAAGACAGGAGGGCCGGGAAACCUGCCUAAUCCAAUGACGGGUAAUAGUGUc  62
                            |       10        20        30        40        50        60 |
                            1-GTP                                                       62-CCC

Chain H from PDB  Type:RNA  Length:62
                                                                                              
                 3rw6 H   1 gGCACUAACCUAAGACAGGAGGGCCGGGAAACCUGCCUAAUCCAAUGACGGGUAAUAGUGUc  62
                            |       10        20        30        40        50        60 |
                            |                                                           62-CCC
                            1-GTP

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 3RW6)

(no "CATH Domain" information available for 3RW6)

(no "Pfam Domain" information available for 3RW6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NXF1_HUMAN | Q9UBU9)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0005487	nucleocytoplasmic transporter activity	Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
biological process
	GO:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0042405	nuclear inclusion body	An intranuclear focus at which aggregated proteins have been sequestered.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0000346	transcription export complex	The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans.

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	3rw6
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(no "Related Entries Specified in the PDB File" available for 3RW6)

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