2WJV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN NONSENSE MEDIATED DECAY FACTORS UPF1 AND UPF2

Authors :   M. Clerici, A. Mourao, I. Gutsche, N. H. Gehring, M. W. Hentze, A. Kulozi J. Kadlec, M. Sattler, S. Cusack

Date :   01 Jun 09 (Deposition) - 07 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Hydrolase, Zinc-Finger, Atp-Binding, Rna-Binding, Nonsense-Mediated Mrna Decay, Nucleotide-Binding, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Clerici, A. Mourao, I. Gutsche, N. H. Gehring, M. W. Hentze, A. Kulozik, J. Kadlec, M. Sattler, S. Cusack
Unusual Bipartite Mode Of Interaction Between The Nonsense-Mediated Decay Factors, Upf1 And Upf2.
Embo J. V. 28 2293 2009
PubMed-ID: 19556969 | Reference-DOI: 10.1038/EMBOJ.2009.175

Molecule 1 - REGULATOR OF NONSENSE TRANSCRIPTS 1
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PCDF-DUET1
	Fragment	:	CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UPF1, ATP-DEPENDENT HELICASE RENT1, NONSENSE MRNA REDUCING FACTOR 1, UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG, NORF1, HUPF1

Molecule 2 - REGULATOR OF NONSENSE TRANSCRIPTS 2
	Chains	:	D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 STAR(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PPROEXHTB
	Fragment	:	C-TERMINAL REGION, RESIDUES 1105-1198
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UPF2, NONSENSE MRNA REDUCING FACTOR 2, UP-FRAMESHIFT SUPPRESSOR 2 HOMOLOG, HUPF2

		1	2	3	4
Asymmetric Unit	:	A	B	D	E
Biological Unit 1 (1x)	:	A		D
Biological Unit 2 (1x)	:		B		E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 29)

No.	Name	Count	Type	Full Name
1	SO4	23	Ligand/Ion	SULFATE ION
2	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 13)

No.	Name	Count	Type	Full Name
1	SO4	13	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	SO4	10	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (29, 29)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:123 , CYS A:126 , CYS A:145 , HIS A:155	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	CYS A:137 , SER A:140 , HIS A:159 , CYS A:165	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	CYS A:183 , CYS A:186 , CYS A:209 , CYS A:213	BINDING SITE FOR RESIDUE ZN A 3
04	AC4	SOFTWARE	GLY A:497 , LYS A:498 , THR A:499 , VAL A:500	BINDING SITE FOR RESIDUE SO4 A 987
05	AC5	SOFTWARE	GLY A:901 , PRO A:902 , ARG A:907	BINDING SITE FOR RESIDUE SO4 A 988
06	AC6	SOFTWARE	MET A:357 , SER A:523 , ASN A:524 , ILE A:525 , ARG A:549	BINDING SITE FOR RESIDUE SO4 A 989
07	AC7	SOFTWARE	PRO A:494 , GLN A:665 , ARG A:703 , GLY A:831 , ARG A:865	BINDING SITE FOR RESIDUE SO4 A 990
08	AC8	SOFTWARE	TYR A:764 , ARG A:843 , HIS A:847 , GLN A:848 , GLY A:849	BINDING SITE FOR RESIDUE SO4 A 991
09	AC9	SOFTWARE	ARG A:767	BINDING SITE FOR RESIDUE SO4 A 992
10	BC1	SOFTWARE	ARG A:832	BINDING SITE FOR RESIDUE SO4 A 993
11	BC2	SOFTWARE	ASN A:472 , HIS A:473	BINDING SITE FOR RESIDUE SO4 A 994
12	BC3	SOFTWARE	ARG A:462 , PHE A:463 , THR A:464	BINDING SITE FOR RESIDUE SO4 A 995
13	BC4	SOFTWARE	THR A:794 , PRO A:795 , SER A:825 , VAL A:826 , ASP A:827 , GLY A:851 , PHE A:852 , ARG A:858	BINDING SITE FOR RESIDUE SO4 A 996
14	BC5	SOFTWARE	SER A:763 , PRO A:795 , TYR A:796 , GLU A:797 , ILE A:850	BINDING SITE FOR RESIDUE SO4 A 997
15	BC6	SOFTWARE	THR A:418 , ARG A:422 , PRO A:623	BINDING SITE FOR RESIDUE SO4 A 998
16	BC7	SOFTWARE	LEU A:544 , CYS A:545 , ALA A:546 , GLU A:550 , LEU A:561 , HIS A:562 , ARG A:624	BINDING SITE FOR RESIDUE SO4 A 999
17	BC8	SOFTWARE	CYS B:123 , CYS B:126 , CYS B:145 , HIS B:155	BINDING SITE FOR RESIDUE ZN B 1
18	BC9	SOFTWARE	CYS B:137 , SER B:140 , HIS B:159 , CYS B:165	BINDING SITE FOR RESIDUE ZN B 2
19	CC1	SOFTWARE	CYS B:183 , CYS B:186 , CYS B:209 , CYS B:213	BINDING SITE FOR RESIDUE ZN B 3
20	CC2	SOFTWARE	ASN B:472 , HIS B:473	BINDING SITE FOR RESIDUE SO4 B 989
21	CC3	SOFTWARE	GLY B:497 , THR B:499 , VAL B:500	BINDING SITE FOR RESIDUE SO4 B 990
22	CC4	SOFTWARE	TYR B:764 , ARG B:843 , HIS B:847 , GLN B:848 , GLY B:849	BINDING SITE FOR RESIDUE SO4 B 991
23	CC5	SOFTWARE	ARG B:767	BINDING SITE FOR RESIDUE SO4 B 992
24	CC6	SOFTWARE	ARG B:832	BINDING SITE FOR RESIDUE SO4 B 993
25	CC7	SOFTWARE	ARG B:462 , PHE B:463 , THR B:464	BINDING SITE FOR RESIDUE SO4 B 995
26	CC8	SOFTWARE	THR B:794 , PRO B:795 , SER B:825 , VAL B:826 , ASP B:827 , GLY B:851 , PHE B:852 , ARG B:858	BINDING SITE FOR RESIDUE SO4 B 996
27	CC9	SOFTWARE	SER B:763 , PRO B:795 , TYR B:796 , GLU B:797 , ILE B:850	BINDING SITE FOR RESIDUE SO4 B 997
28	DC1	SOFTWARE	SER B:523 , ASN B:524 , ILE B:525 , ARG B:549	BINDING SITE FOR RESIDUE SO4 B 998
29	DC2	SOFTWARE	PRO B:494 , GLN B:665 , ARG B:703 , GLY B:831 , ARG B:865	BINDING SITE FOR RESIDUE SO4 B 999

(no "SS Bond" information available for 2WJV)

Asymmetric Unit

No.	Residues
1	Gln A:211	-	Pro A:212
2	Gln B:211	-	Pro B:212

(no "SAP(SNP)/Variant" information available for 2WJV)

(no "PROSITE Motif" information available for 2WJV)

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000397053	1b	ENSE00001402467	chr10:12085023-12084913	111	RENT2_HUMAN	-	0	0	-	-
1.3c	ENST00000397053	3c	ENSE00002187710	chr10:12077440-12077058	383	RENT2_HUMAN	1-122	122	0	-	-
1.4	ENST00000397053	4	ENSE00000999707	chr10:12071523-12070744	780	RENT2_HUMAN	122-382	261	0	-	-
1.5	ENST00000397053	5	ENSE00001349465	chr10:12056183-12056023	161	RENT2_HUMAN	382-436	55	0	-	-
1.6	ENST00000397053	6	ENSE00001213473	chr10:12046726-12046529	198	RENT2_HUMAN	436-502	67	0	-	-
1.7	ENST00000397053	7	ENSE00001213468	chr10:12043824-12043675	150	RENT2_HUMAN	502-552	51	0	-	-
1.8b	ENST00000397053	8b	ENSE00001213463	chr10:12042008-12041905	104	RENT2_HUMAN	552-586	35	0	-	-
1.9	ENST00000397053	9	ENSE00001754391	chr10:12039756-12039671	86	RENT2_HUMAN	587-615	29	0	-	-
1.10	ENST00000397053	10	ENSE00001649308	chr10:12021164-12021056	109	RENT2_HUMAN	615-651	37	0	-	-
1.11	ENST00000397053	11	ENSE00001649100	chr10:12009453-12009340	114	RENT2_HUMAN	652-689	38	0	-	-
1.12	ENST00000397053	12	ENSE00001742008	chr10:12006124-12006008	117	RENT2_HUMAN	690-728	39	0	-	-
1.13	ENST00000397053	13	ENSE00001617394	chr10:12001355-12001170	186	RENT2_HUMAN	729-790	62	0	-	-
1.14	ENST00000397053	14	ENSE00001724518	chr10:11998522-11998319	204	RENT2_HUMAN	791-858	68	0	-	-
1.15	ENST00000397053	15	ENSE00001595330	chr10:11997506-11997231	276	RENT2_HUMAN	859-950	92	0	-	-
1.16	ENST00000397053	16	ENSE00001647744	chr10:11994248-11994065	184	RENT2_HUMAN	951-1012	62	0	-	-
1.17	ENST00000397053	17	ENSE00001662463	chr10:11990507-11990368	140	RENT2_HUMAN	1012-1058	47	0	-	-
1.18	ENST00000397053	18	ENSE00001754512	chr10:11985167-11985063	105	RENT2_HUMAN	1059-1093	35	0	-	-
1.19	ENST00000397053	19	ENSE00001760455	chr10:11984762-11984664	99	RENT2_HUMAN	1094-1126	33	2	D:1102-1126 (gaps) E:1102-1126 (gaps)	30 30
1.20	ENST00000397053	20	ENSE00001094605	chr10:11978711-11978544	168	RENT2_HUMAN	1127-1182	56	2	D:1127-1182 (gaps) E:1127-1182 (gaps)	56 56
1.21b	ENST00000397053	21b	ENSE00001094602	chr10:11973781-11973640	142	RENT2_HUMAN	1183-1230	48	2	D:1183-1198 E:1183-1198	16 16
1.22	ENST00000397053	22	ENSE00001094595	chr10:11971984-11971864	121	RENT2_HUMAN	1230-1270	41	0	-	-
1.23a	ENST00000397053	23a	ENSE00001213550	chr10:11963306-11962022	1285	RENT2_HUMAN	1270-1272	3	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:772
 aligned with RENT1_HUMAN | Q92900 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:807
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       
         RENT1_HUMAN    116 KDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLM  922
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhh.eeee....eeee........hhhhhhhhhhh...eee.......................eeeee.....eeeeee...........---.hhhhhee.ee..ee........hhhhhhhh...hhhhhhhhhhhh...........-----............hhhhhhhhhhhhhhhhhhhhhhhhh...eeee.eeeehhhhh..eeee...------------------.....eeeeee.......eeeeeeeee..----..eeee-----.........eeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhh.........................hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh....eee..hhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh.....eeee.hhhhhhhhhhhhhhh....eeeeee..........hhhhhhh....hhhhhhhhhh...ee..ee...hhhhhhhhhhhhh....ee...hhhhh..............eeeee.....eee....eeehhhhhhhhhhhhhhhhhhh.hhh.eeee..hhhhhhhhhhhhhhhh..hhhhhhh.eee.hhhhh...eeeeeee.........hhhhhhhhhhhhhh..eeeeeeeeehhhhhh.hhhhhhhhhhhhhh..eee.hhhhhee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wjv A  116 KDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLK---WDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDL-----DEEPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLP------------------LMQGDEICLRYKGDLAPLWKGIGHVIKVP----DEIAIE-----GAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLM  911
                                   125       135       145       155       165       175       185       195       205       215    |  225       235       245       255       265       275    |    -|      295       305       315       325       335       345  |      -         - |     364       374       384    |  394     | 404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       
                                                                                                                                  220 224                                                     280   286                                                           348                356                         384  389  394   400

Chain B from PDB  Type:PROTEIN  Length:768
 aligned with RENT1_HUMAN | Q92900 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:809
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915         
         RENT1_HUMAN    116 KDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQF  924
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----UPF1_Zn_bind-2wjvB05 B:121-272                                                                                                                          --------       ----------------------------------------------      ---------                  -----------------------------    ---------------------------------------------------------------------------------AAA_11-2wjvB01 B:470-673                                                                                                                                                                                    ------AAA_12-2wjvB03 B:680-877                                                                                                                                                                              ------------------------------------ Pfam domains (1)
           Pfam domains (2) -----UPF1_Zn_bind-2wjvB06 B:121-272                                                                                                                          --------       ----------------------------------------------      ---------                  -----------------------------    ---------------------------------------------------------------------------------AAA_11-2wjvB02 B:470-673                                                                                                                                                                                    ------AAA_12-2wjvB04 B:680-877                                                                                                                                                                              ------------------------------------ Pfam domains (2)
         Sec.struct. author ..............hhh.eeee....eeee........hhhhhhhhhhh...eee.......................eeeee.....eeeeee.hhhhh.....---.hhhhhee.ee..ee........hhhhhhhh...hhhhhhhhhhhh......hhhhh-------..........hhhhhhhhhhhhhhhhhhhhhhhhh...eeee.ee.------..eeee...------------------.....eeeeee.......eeeeeeeee..----..eeeee.............eeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhh.........................hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh...eee..hhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh.....eeee.hhhhhhhhhhhhhhh....eeeeee..........hhhhhhh....hhhhhhhhhh...ee..ee...hhhhhhhhhhhhh....ee......................eeeee.......---.....hhhhhhhhhhhhhhhhhhh.hhh.eeee..hhhhhhhhhhhhhhhh..hhhhhhh.eeehhhhhh...eeeeeee.........hhhhhhhhhhhhhh..eeeeeeeeehhhhhh.hhhhhhhhhhhhhh..eee.hhhhhee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wjv B  116 KDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLK---WDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDL-------EPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRW------KRIAYFTLP------------------LMQGDEICLRYKGDLAPLWKGIGHVIKVP----DEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEI---GTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQF  913
                                   125       135       145       155       165       175       185       195       205       215    |  225       235       245       255       265       275    |    -  |    295       305       315       325       | -    |  345  |      -         - |     364       374       384    |  394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754  |   |764       774       784       794       804       814       824       834       844       854       864       874       884       894       904         
                                                                                                                                  220 224                                                     280     288                                          333    340     348                356                         384  389                                                                                                                                                                                                                                                                                                                                                                             757 761

Chain D from PDB  Type:PROTEIN  Length:54
 aligned with RENT2_HUMAN | Q9HAU5 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:102
                                  1106      1116      1126      1136      1146      1156      1166      1176      1186      1196  
         RENT2_HUMAN   1097 IKGGGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQLRKGPPLGGGEGEAESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANH 1198
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...-----..hhhhhhhhhhhhhhhhhhhhh.--------------------------------------.eeeeeee.-----..eeeeeee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.19 UniProt: 1094-1126  Exon 1.20  PDB: D:1127-1182 (gaps) UniProt: 1127-1182   Exon 1.21b       Transcript 1
                2wjv D 1102 AMG-----VPCVEDEDFIQALDKMMLENLQQR--------------------------------------DTMPFVMLT-----QQFKILNVPMSSQLAANH 1198
                              |   1106      1116      1126 |       -         -         -         -|       |-    | 1186      1196  
                           1104  1105                   1128                                   1167    1175  1181

Chain E from PDB  Type:PROTEIN  Length:60
 aligned with RENT2_HUMAN | Q9HAU5 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:102
                                  1106      1116      1126      1136      1146      1156      1166      1176      1186      1196  
         RENT2_HUMAN   1097 IKGGGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQLRKGPPLGGGEGEAESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANH 1198
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---     Upf2-2wjvE01 E:1105-1198                                                                       Pfam domains (1)
           Pfam domains (2) ---     Upf2-2wjvE02 E:1105-1198                                                                       Pfam domains (2)
         Sec.struct. author ...-----..hhhhhhhhhhhhhhhhhhhhhhh-------------------------------------.eeeeeeeeee..eeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.19 UniProt: 1094-1126  Exon 1.20  PDB: E:1127-1182 (gaps) UniProt: 1127-1182   Exon 1.21b       Transcript 1
                2wjv E 1102 AMG-----VPCVEDEDFIQALDKMMLENLQQRS-------------------------------------DTMPFVMLTRKGNKQQFKILNVPMSSQLAANH 1198
                              |   1106      1116      1126  |      -         -         -         -|     1176      1186      1196  
                           1104  1105                    1129                                  1167

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 2WJV)

(no "CATH Domain" information available for 2WJV)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AAA_11 (5)

Homo sapiens (Human) (4)

1a	AAA_11-2wjvB01	B:470-673
1b	AAA_11-2wjvB02	B:470-673

Family: AAA_12 (5)

Homo sapiens (Human) (4)

2a	AAA_12-2wjvB03	B:680-877
2b	AAA_12-2wjvB04	B:680-877

Clan: TPR (230)

Family: Upf2 (1)

Homo sapiens (Human) (1)

3a	Upf2-2wjvE01	E:1105-1198
3b	Upf2-2wjvE02	E:1105-1198

Clan: no clan defined [family: UPF1_Zn_bind] (3)

Family: UPF1_Zn_bind (3)

Homo sapiens (Human) (2)

4a	UPF1_Zn_bind-2wjvB05	B:121-272
4b	UPF1_Zn_bind-2wjvB06	B:121-272

Asymmetric Unit(hide GO term definitions)

Chain A,B (RENT1_HUMAN | Q92900)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0061158	3'-UTR-mediated mRNA destabilization	An mRNA destabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0071347	cellular response to interleukin-1	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0009048	dosage compensation by inactivation of X chromosome	Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex.
	GO:0071044	histone mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of histone messenger RNA (mRNA).
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0000956	nuclear-transcribed mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
	GO:0000294	nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay	A minor degradation pathway nuclear-transcribed mRNAs that begins with an endonucleolytic cleavage to generate unprotected ends.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0061014	positive regulation of mRNA catabolic process	Any process that increases the rate, frequency, or extent of a mRNA catabolic process, the chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0006449	regulation of translational termination	Any process that modulates the frequency, rate or extent of translational termination.
	GO:0000723	telomere maintenance	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
	GO:0032201	telomere maintenance via semi-conservative replication	The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	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:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	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:0044530	supraspliceosomal complex	Multicomponent complex of RNA and proteins that is composed of four active spliceosomes, termed native spliceosomes, connected to each other by the pre-mRNA. The supraspliceosome is the nuclear machine where the pre-mRNA processing takes place, like the 5'-end capping, 3'-end cleavage, splicing and editing.

Chain D,E (RENT2_HUMAN | Q9HAU5)

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).
	GO:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
biological process
	GO:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
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:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	Cis Peptide Bonds
		Gln A:211 - Pro A:212	[ RasMol ]
		Gln B:211 - Pro B:212	[ RasMol ]

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	2wjv
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	RENT1_HUMAN \| Q92900
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	RENT2_HUMAN \| Q9HAU5
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	RENT1_HUMAN \| Q92900
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	RENT2_HUMAN \| Q9HAU5
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UniProtKB/Swiss-Prot
	RENT1_HUMAN \| Q92900	:	2gjk 2gk6 2gk7 2iyk 2wjy 2xzo 2xzp
	RENT2_HUMAN \| Q9HAU5	:	1uw4 4cek 4cem

1uw4	THE STRUCTURAL BASIS OF THE INTERACTION BETWEEN NONSENSE MEDIATED DECAY FACTORS UPF2 AND UPF3
2iyk	CRYSTAL STRUCTURE OF THE UPF2-INTERACTING DOMAIN OF NONSENSE MEDIATED MRNA DECAY FACTOR UPF1
2wjy	CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN NONSENSE MEDIATED DECAY FACTORS UPF1 AND UPF2 ORTHORHOMBIC FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 29)

Sites (29, 29)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (4, 8)

Gene Ontology (39, 48)

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