3NV0 - JenaLib

Title :   CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF THE NXF2/NXT1 HETERODIMERIC COMPLEX FROM CAENORHABDITIS ELEGANS AT 1.84 A RESOLUTION

Authors :   D. E. Kerkow, A. B. Carmel, J. R. Williamson

Date :   07 Jul 10 (Deposition) - 20 Jul 11 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

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

Keywords :   Ntf2-Like Domain, Beta Sheet Heterodimer Interface, Nucleoporin Binding Pocket, Water Mediated Interface, Cation-Pi Interactions, Pi-Pi Interactions, Nxf-Loop, Ntf2-Plug, Intramonomer Buried Waters, Novel Surface Exposed Pockets, Mrna Transport, Nucleus, Rna-Binding, Rna Binding-Protein Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. E. Kerkow, A. B. Carmel, E. Menichelli, G. Ambrus, R. D. Hills, L. Gerace, J. R. Williamson
The Structure Of The Nxf2/Nxt1 Heterodimeric Complex Reveal The Combined Specificity And Versatility Of The Ntf2-Like Fold.
J. Mol. Biol. V. 415 649 2012
PubMed-ID: 22123199 | Reference-DOI: 10.1016/J.JMB.2011.11.027

Compounds

Molecule 1 - NUCLEAR RNA EXPORT FACTOR 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET-1
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NTF2-LIKE DOMAIN (UNP RESIDUES 218-421)
	Gene	:	C15H11.6, NXF-2
	Organism Common	:	NEMATODE
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239

Molecule 2 - NTF2-RELATED EXPORT PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET-1
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NXT-1, NXT1, Y71F9AM.5
	Organism Common	:	NEMATODE
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 26)

Sites (26, 26)

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:294 , ILE A:296 , HIS A:298 , ILE B:9 , GLU B:12 , ASP B:13 , HOH B:503	BINDING SITE FOR RESIDUE PEG A 1001
02	AC2	SOFTWARE	LEU A:215 , ARG A:277 , TYR A:287 , ARG A:292 , ARG A:295 , GLU A:370 , GLY A:371 , NA A:456 , HOH A:553	BINDING SITE FOR RESIDUE PEG A 1002
03	AC3	SOFTWARE	ASP A:268 , GLU A:270 , GLY A:343 , PRO A:344 , ILE A:347 , HOH A:625	BINDING SITE FOR RESIDUE EDO A 1003
04	AC4	SOFTWARE	ASP A:228 , THR A:235 , HOH A:555 , HOH A:586 , HOH A:665	BINDING SITE FOR RESIDUE NA A 450
05	AC5	SOFTWARE	ASP A:259 , ILE A:261 , SER A:386 , ARG A:388 , HOH A:507	BINDING SITE FOR RESIDUE NA A 451
06	AC6	SOFTWARE	TYR A:358 , TYR A:393 , HOH A:564 , TYR B:135 , VAL B:136	BINDING SITE FOR RESIDUE NA A 452
07	AC7	SOFTWARE	GLN A:238	BINDING SITE FOR RESIDUE NA A 453
08	AC8	SOFTWARE	SER A:294 , ARG A:295 , HOH A:552 , HOH A:654	BINDING SITE FOR RESIDUE NA A 454
09	AC9	SOFTWARE	ASP A:228 , HIS A:315 , HOH A:633 , HOH A:634	BINDING SITE FOR RESIDUE NA A 455
10	BC1	SOFTWARE	ARG A:292 , ALA A:293 , ARG A:295 , GLU A:370 , PEG A:1002	BINDING SITE FOR RESIDUE NA A 456
11	BC2	SOFTWARE	TYR A:206 , PRO B:54 , ASN B:56	BINDING SITE FOR RESIDUE NA A 457
12	BC3	SOFTWARE	GLN A:238 , LEU A:240 , ASP A:241 , HOH A:669 , GLY B:86	BINDING SITE FOR RESIDUE NA A 458
13	BC4	SOFTWARE	GLU A:270 , ARG A:273 , MET A:274 , ARG A:277	BINDING SITE FOR RESIDUE NA A 459
14	BC5	SOFTWARE	ARG A:341 , ASP A:342 , SER A:345 , HIS A:355 , ASN A:357 , HOH A:582	BINDING SITE FOR RESIDUE NA A 460
15	BC6	SOFTWARE	GLU A:286 , HOH A:670 , GLU B:14 , CYS B:17 , ASN B:18	BINDING SITE FOR RESIDUE BME B 1001
16	BC7	SOFTWARE	PRO B:54 , ILE B:55 , ASN B:56 , SER B:60 , HOH B:546	BINDING SITE FOR RESIDUE PEG B 1002
17	BC8	SOFTWARE	ARG B:35 , MET B:65 , LYS B:66 , LEU B:68 , PRO B:69 , SER B:70 , HOH B:506 , HOH B:553 , HOH B:573	BINDING SITE FOR RESIDUE PEG B 1003
18	BC9	SOFTWARE	THR A:330 , HOH A:652 , VAL B:87 , THR B:88 , MET B:91 , HOH B:579 , HOH B:580 , HOH B:584	BINDING SITE FOR RESIDUE PEG B 1004
19	CC1	SOFTWARE	LYS A:262 , PHE A:263 , HOH A:612 , ASP B:108 , HOH B:517	BINDING SITE FOR RESIDUE NA B 450
20	CC2	SOFTWARE	PHE B:40 , LYS B:125 , LYS B:127 , HOH B:575	BINDING SITE FOR RESIDUE NA B 451
21	CC3	SOFTWARE	THR A:253 , LEU A:380 , ASP B:79 , ASN B:98	BINDING SITE FOR RESIDUE NA B 452
22	CC4	SOFTWARE	ASP B:25 , HOH B:531 , HOH B:605	BINDING SITE FOR RESIDUE NA B 453
23	CC5	SOFTWARE	GLN B:44 , VAL B:45 , SER B:46 , GLY B:57 , TYR B:58 , HOH B:501	BINDING SITE FOR RESIDUE NA B 454
24	CC6	SOFTWARE	PRO A:349 , HOH A:677 , ARG B:82 , GLY B:93 , TYR B:126 , HOH B:572	BINDING SITE FOR RESIDUE NA B 455
25	CC7	SOFTWARE	ASP B:90 , MET B:91 , LYS B:129 , HOH B:584	BINDING SITE FOR RESIDUE NA B 456
26	CC8	SOFTWARE	ASP B:90 , GLU B:122 , HOH B:542 , HOH B:554	BINDING SITE FOR RESIDUE NA B 457

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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:PROTEIN  Length:196
 aligned with NXF2_CAEEL | Q9XVS8 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:196
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406      
           NXF2_CAEEL   217 PFRNGYYGSDEVRTLVEEFIITYYKIYDGADGQQTRKQLLDAYDTNNSTFTHTVVCLWDPIKFVMYPDSESYRMYLRTSHNVLNQEYFAANRASRISHGAMDIVVALSRLPATIHLMDTFVVDVFLVSATLLGFTLHGTFRDGPSAIKPENTEEHDNYFTRTFMVAPRGEGKVAIVSDQLFISSMSKRRGDQYRML 412
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeee............hhhhhhhhhhh..hhhhh...........eehhhhhhhhhhhh..eee.hhhheeeeeee....eeeeeeeeeeehhhhhh........eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------NTF2_DOMAIN  PDB: A:215-382 UniProt: 231-398                                                                                                                            -------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nv0 A 201 MFRNGYYGSDEVRTLVEEFIITYYKIYDGADGQQTRKQLLDAYDTNNSTFTHTVVCLWDPIKFVMYPDSESYRMYLRTSHNVLNQEYFAANRASRISHGAMDIVVALSRLPATIHLMDTFVVDVFLVSATLLGFTLHGTFRDGPSAIKPENTEEHDNYFTRTFMVAPRGEGKVAIVSDQLFISSMSKRRGDQYRML 396
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

Chain B from PDB  Type:PROTEIN  Length:136
 aligned with NXT1_CAEEL | Q9U757 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      
           NXT1_CAEEL     2 SMKTTQEINKEDEELCNESKKFMDVYYDVMDRKREKIGFLYTQVSNAVWNGNPINGYDSICEFMKALPSTQHDIQSLDAQRLPEGVTGDMSGGMLLNVAGAVTVDGDSKRAFTQTLLLGVEDGKYKVKSDRFRYVD 137
               SCOP domains d3nv0b_ B: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeehhhhhhhhhhhh..eeeeeeeeeeee.....hhhhh..eeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------NTF2_DOMAIN  PDB: B:19-135 UniProt: 19-135                                                                           -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nv0 B   2 SMKTTQEINKEDEELCNESKKFMDVYYDVMDRKREKIGFLYTQVSNAVWNGNPINGYDSICEFMKALPSTQHDIQSLDAQRLPEGVTGDMSGGMLLNVAGAVTVDGDSKRAFTQTLLLGVEDGKYKVKSDRFRYVD 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NXF2_CAEEL | Q9XVS8)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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).
biological process
	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.
cellular component
	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.

Chain B (NXT1_CAEEL | Q9U757)

molecular function
	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).
biological process
	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:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
cellular component
	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: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.

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