1CVJ | PR0007 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

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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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Biological Unit 8 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN COMPLEX WITH POLYADENYLATE RNA

Authors :   R. C. Deo, J. B. Bonanno, N. Sonenberg, S. K. Burley

Date :   23 Aug 99 (Deposition) - 04 Oct 99 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,M,N,O,P,Q,R,S,T
Biol. Unit 1: A,M  (1x)
Biol. Unit 2: B,N  (1x)
Biol. Unit 3: C,O  (1x)
Biol. Unit 4: D,P  (1x)
Biol. Unit 5: E,Q  (1x)
Biol. Unit 6: F,R  (1x)
Biol. Unit 7: G,S  (1x)
Biol. Unit 8: H,T  (1x)

Keywords :   Rrm, Protein-Rna Complex, Gene Regulation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. C. Deo, J. B. Bonanno, N. Sonenberg, S. K. Burley
Recognition Of Polyadenylate Rna By The Poly(A)-Binding Protein.
Cell(Cambridge, Mass. ) V. 98 835 1999
PubMed-ID: 10499800 | Reference-DOI: 10.1016/S0092-8674(00)81517-2

*Molecule 1 - 5'-R(APAPAPAPAPAPAPAPAPAPA)-3'**
	Chains	:	M, N, O, P, Q, R, S, T
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - POLYADENYLATE BINDING PROTEIN 1
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-190
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POLY(A) BINDING PROTEIN 1, PABP 1

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	B	C	D	E	F	G	H	M	N	O	P	Q	R	S	T
Biological Unit 1 (1x)	:	A								M
Biological Unit 2 (1x)	:		B								N
Biological Unit 3 (1x)	:			C								O
Biological Unit 4 (1x)	:				D								P
Biological Unit 5 (1x)	:					E								Q
Biological Unit 6 (1x)	:						F								R
Biological Unit 7 (1x)	:							G								S
Biological Unit 8 (1x)	:								H								T

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	A	8	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 7 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Biological Unit 8 (0, 0)

No.	Name	Count	Type	Full Name
1	A	-1	Ligand/Ion	ADENOSINE-5'-MONOPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:58 , A M:8	BINDING SITE FOR RESIDUE A A 991
2	AC2	SOFTWARE	A N:6	BINDING SITE FOR RESIDUE A N 992
3	AC3	SOFTWARE	A O:6	BINDING SITE FOR RESIDUE A O 993
4	AC4	SOFTWARE	ASN D:58	BINDING SITE FOR RESIDUE A D 994
5	AC5	SOFTWARE	A Q:7	BINDING SITE FOR RESIDUE A Q 995
6	AC6	SOFTWARE	A R:6	BINDING SITE FOR RESIDUE A F 996
7	AC7	SOFTWARE	ASN G:58 , A S:6	BINDING SITE FOR RESIDUE A S 997
8	AC8	SOFTWARE	SER H:39 , ASN H:58	BINDING SITE FOR RESIDUE A H 998

(no "SS Bond" information available for 1CVJ)

(no "Cis Peptide Bond" information available for 1CVJ)

(no "SAP(SNP)/Variant" information available for 1CVJ)

Asymmetric Unit (1, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	16	A:11-89 B:11-89 C:11-89 D:11-89 E:11-89 F:11-89 G:11-89 H:11-89 A:99-175 B:99-175 C:99-175 D:99-175 E:99-175 F:99-173 G:99-175 H:99-175 - -

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	A:11-89 - - - - - - - A:99-175 - - - - - - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- B:11-89 - - - - - - - B:99-175 - - - - - - - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- - C:11-89 - - - - - - - C:99-175 - - - - - - -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- - - D:11-89 - - - - - - - D:99-175 - - - - - -

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- - - - E:11-89 - - - - - - - E:99-175 - - - - -

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- - - - - F:11-89 - - - - - - - F:99-173 - - - -

Biological Unit 7 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- - - - - - G:11-89 - - - - - - - G:99-175 - - -

Biological Unit 8 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PABP1_HUMAN	11-89 99-175 191-268 294-370	2	- - - - - - - H:11-89 - - - - - - - H:99-175 - -

Asymmetric Unit (4, 32)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1e	ENST00000318607	1e	ENSE00002107718	chr8:101734940-101733619	1322	PABP1_HUMAN	1-65	65	8	A:11-65 B:11-65 C:11-65 D:11-65 E:11-65 F:11-65 G:11-65 H:11-65	55 55 55 55 55 55 55 55
1.2e	ENST00000318607	2e	ENSE00002179154	chr8:101730508-101730315	194	PABP1_HUMAN	65-129	65	8	A:65-129 B:65-129 C:65-129 D:65-129 E:65-129 F:65-129 (gaps) G:65-129 H:65-129 (gaps)	65 65 65 65 65 65 65 65
1.2i	ENST00000318607	2i	ENSE00001088711	chr8:101730116-101730001	116	PABP1_HUMAN	130-168	39	8	A:130-168 B:130-159 (gaps) C:130-168 D:130-168 (gaps) E:130-168 F:130-168 (gaps) G:130-168 H:130-152 (gaps)	39 30 39 39 39 39 39 23
1.3b	ENST00000318607	3b	ENSE00001676241	chr8:101727829-101727690	140	PABP1_HUMAN	168-215	48	8	A:168-179 B:170-175 C:168-178 D:168-175 E:168-178 F:168-173 G:168-175 H:173-175	12 6 11 8 11 6 8 3
1.4c	ENST00000318607	4c	ENSE00001088702	chr8:101725409-101725315	95	PABP1_HUMAN	215-246	32	0	-	-
1.5a	ENST00000318607	5a	ENSE00001088717	chr8:101725017-101724880	138	PABP1_HUMAN	247-292	46	0	-	-
1.6a	ENST00000318607	6a	ENSE00001088710	chr8:101724685-101724590	96	PABP1_HUMAN	293-324	32	0	-	-
1.7b	ENST00000318607	7b	ENSE00002184139	chr8:101721959-101721687	273	PABP1_HUMAN	325-415	91	0	-	-
1.8c	ENST00000318607	8c	ENSE00001088708	chr8:101721451-101721361	91	PABP1_HUMAN	416-446	31	0	-	-
1.9b	ENST00000318607	9b	ENSE00001088705	chr8:101719225-101719115	111	PABP1_HUMAN	446-483	38	0	-	-
1.10b	ENST00000318607	10b	ENSE00002199412	chr8:101719033-101718879	155	PABP1_HUMAN	483-534	52	0	-	-
1.11	ENST00000318607	11	ENSE00001088703	chr8:101717901-101717817	85	PABP1_HUMAN	535-563	29	0	-	-
1.12a	ENST00000318607	12a	ENSE00001088713	chr8:101717284-101717154	131	PABP1_HUMAN	563-606	44	0	-	-
1.13a	ENST00000318607	13a	ENSE00001088716	chr8:101716618-101716525	94	PABP1_HUMAN	607-636	30	0	-	-
1.14e	ENST00000318607	14e	ENSE00001378950	chr8:101715587-101715144	444	PABP1_HUMAN	-	0	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:169
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:169
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER 179
               SCOP domains d1cvja1 A:11-90 Poly(A)-binding protein                                         d1cvja2 A:91-179 Poly(A)-binding protein                                                  SCOP domains
               CATH domains 1cvjA01 A:11-87  [code=3.30.70.330, no name defined]                         1cvjA02 A:88-179  [code=3.30.70.330, no name defined]                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhh.....ee..ee.eeee....hhhhhh...eeeee......hhhhhhhhhhh...eeeeee..........eeeee.hhhhhhhhh....eeee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: A:11-89 UniProt: 11-89                                               ---------RRM  PDB: A:99-175 UniProt: 99-175                                           ---- PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: A:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: A:130-168              ----------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: A:65-129 UniProt: 65-129                         --------------------------------------Exon 1.3b    Transcript 1 (2)
                 1cvj A  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER 179
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:165
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
               SCOP domains d1cvjb1 B:11-90 Poly(A)-binding protein                                         d1cvjb2 B:91-175 Poly(A)-binding protein                                              SCOP domains
               CATH domains 1cvjB01 B:11-87  [code=3.30.70.330, no name defined]                         1cvjB02 B:88-173  [code=3.30.70.330, no name     defined]                             -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh...eeee.......hhhhhhhhhhh...eeeeee..----....eeeee.hhhhhhhhh....----------.ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: B:11-89 UniProt: 11-89                                               ---------RRM  PDB: B:99-175 UniProt: 99-175                                            PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: B:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: B:130-159 (gaps)       ------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: B:65-129 UniProt: 65-129                         --------------------------------------1.3b     Transcript 1 (2)
                 1cvj B  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC----SKGYGFVHFETQEAAERAIEKMN----------VGRFKS 175
                                    20        30        40        50        60        70        80        90       100       110       120       130 |    |140       150        |-       170     
                                                                                                                                                   132  137                   159        170

Chain C from PDB  Type:PROTEIN  Length:168
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:168
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178
               SCOP domains d1cvjc1 C:11-90 Poly(A)-binding protein                                         d1cvjc2 C:91-178 Poly(A)-binding protein                                                 SCOP domains
               CATH domains 1cvjC01 C:11-87  [code=3.30.70.330, no name defined]                         1cvjC02 C:88-178  [code=3.30.70.330, no name defined]                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh...eeeee......hhhhhhhhhhh...eeeeee.........eeeeee.hhhhhhhhhhhh..eee..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE RRM  PDB: C:11-89 UniProt: 11-89                                               ---------RRM  PDB: C:99-175 UniProt: 99-175                                           --- PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: C:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: C:130-168              ---------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: C:65-129 UniProt: 65-129                         --------------------------------------Exon 1.3b   Transcript 1 (2)
                 1cvj C  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:165
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
               SCOP domains d1cvjd1 D:11-90 Poly(A)-binding protein                                         d1cvjd2 D:91-175 Poly(A)-binding protein                                              SCOP domains
               CATH domains 1cvjD01 D:11-87  [code=3.30.70.330, no name defined]                         1cvjD02 D:88-174  [code=3.30.70.330, no name     defined]                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh...eeeee......hhhhhhhhhh....eeeee...----....eeeee.hhhhhhhhhhhh..........eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: D:11-89 UniProt: 11-89                                               ---------RRM  PDB: D:99-175 UniProt: 99-175                                            PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: D:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: D:130-168 (gaps)       ------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: D:65-129 UniProt: 65-129                         --------------------------------------1.3b     Transcript 1 (2)
                 1cvj D  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC----SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
                                    20        30        40        50        60        70        80        90       100       110       120       130 |    |140       150       160       170     
                                                                                                                                                   132  137

Chain E from PDB  Type:PROTEIN  Length:168
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:168
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178
               SCOP domains d1cvje1 E:11-90 Poly(A)-binding protein                                         d1cvje2 E:91-178 Poly(A)-binding protein                                                 SCOP domains
               CATH domains 1cvjE01 E:11-87  [code=3.30.70.330, no name defined]                         1cvjE02 E:88-178  [code=3.30.70.330, no name defined]                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhh.....ee..ee.eeee....hhhhhh...eeeee......hhhhhhhhhh....eeeee...........eeeee.hhhhhhhhhhhh..........eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE RRM  PDB: E:11-89 UniProt: 11-89                                               ---------RRM  PDB: E:99-175 UniProt: 99-175                                           --- PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: E:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: E:130-168              ---------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: E:65-129 UniProt: 65-129                         --------------------------------------Exon 1.3b   Transcript 1 (2)
                 1cvj E  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain F from PDB  Type:PROTEIN  Length:131
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:163
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 173
               SCOP domains d1cvjf1 F:11-90 Poly(A)-binding protein                                         d1cvjf2 F:9          1-173 Poly(A)-binding     protein                              SCOP domains
               CATH domains 1cvjF01 F:11-87  [code=3.30.70.330, no name defined]                         1cvjF02 F:88-1          70  [code=3.30.70.330    , no name def                  ine--- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhh.....ee..ee.eeee....hhhhhh...ee----------.............eee.....----......eee....------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: F:11-89 UniProt: 11-89                                               ---------RRM  PDB: F:99-173 UniProt: 99-175                                          PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: F:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: F:130-168 (gaps)       ----- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: F:65-129 (gaps) UniProt: 65-129                  --------------------------------------1.3b   Transcript 1 (2)
                 1cvj F  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNI----------NKALYDTFSAFGNILSCKVVC----SKGYGFVHFETQE------------------VFVGRF 173
                                    20        30        40        50        60        70        80        90       100|        - |     120       130 |    |140        |-         -       170   
                                                                                                                    101        112                 132  137         149                168

Chain G from PDB  Type:PROTEIN  Length:165
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:165
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
               SCOP domains d1cvjg1 G:11-90 Poly(A)-binding protein                                         d1cvjg2 G:91-175 Poly(A)-binding protein                                              SCOP domains
               CATH domains 1cvjG01 G:11-87  [code=3.30.70.330, no name defined]                         1cvjG02 G:88-175  [code=3.30.70.330, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh...eeeee......hhhhhhhhhhhhh.eeeee...........eeeee.hhhhhhhhhhhh..........eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: G:11-89 UniProt: 11-89                                               ---------RRM  PDB: G:99-175 UniProt: 99-175                                            PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: G:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: G:130-168              ------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: G:65-129 UniProt: 65-129                         --------------------------------------1.3b     Transcript 1 (2)
                 1cvj G  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain H from PDB  Type:PROTEIN  Length:132
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:165
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          PABP1_HUMAN    11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
               SCOP domains d1cvjh1 H:11-90 Poly(A)-binding protein                                         d1cvjh2 H:91-         175 Poly(A)-binding     protein                                 SCOP domains
               CATH domains 1cvjH01 H:11-87  [code=3.30.70.330, no name defined]                         1cvjH02 H:88-152           [code=3.30.70.330,     no name defined                    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhh.....ee..ee.eeee....hhhhhhh..eeee---------hhhhhhhh....eeeeee..----....eeeee.......--------------------... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: H:11-89 UniProt: 11-89                                               ---------RRM  PDB: H:99-175 UniProt: 99-175                                            PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: H:11-65 UniProt: 1-65 [INCOMPLETE]     ----------------------------------------------------------------Exon 1.2i  PDB: H:130-152 (gaps)       ------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2e  PDB: H:65-129 (gaps) UniProt: 65-129                  --------------------------------------1.3b     Transcript 1 (2)
                 1cvj H  11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFI---------KALYDTFSAFGNILSCKVVC----SKGYGFVHFETQEAAE--------------------FKS 175
                                    20        30        40        50        60        70        80        90       100  |      -  |    120       130 |    |140       150 |       -         -  |  
                                                                                                                      103       113                132  137            152                  173

Chain M from PDB  Type:RNA  Length:9
                                         
                 1cvj M   1 AAAAAAAAA   9

Chain N from PDB  Type:RNA  Length:8
                                        
                 1cvj N   1 AAAAAAAA 992
                                  ||
                                  7|
                                 992

Chain O from PDB  Type:RNA  Length:8
                                        
                 1cvj O   1 AAAAAAAA 993
                                  ||
                                  7|
                                 993

Chain P from PDB  Type:RNA  Length:7
                                       
                 1cvj P   1 AAAAAAA   7

Chain Q from PDB  Type:RNA  Length:9
                                         
                 1cvj Q   1 AAAAAAAAA 995
                                   ||
                                   8|
                                  995

Chain R from PDB  Type:RNA  Length:7
                                       
                 1cvj R   1 AAAAAAA   7

Chain S from PDB  Type:RNA  Length:8
                                        
                 1cvj S   1 AAAAAAAA 997
                                  ||
                                  7|
                                 997

Chain T from PDB  Type:RNA  Length:7
                                       
                 1cvj T   1 AAAAAAA   7

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: Poly(A)-binding protein (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1cvja1	A:11-90
1b	d1cvja2	A:91-179
1c	d1cvjf1	F:11-90
1d	d1cvjf2	F:91-173
1e	d1cvjg1	G:11-90
1f	d1cvjg2	G:91-175
1g	d1cvjh1	H:11-90
1h	d1cvjh2	H:91-175
1i	d1cvjb1	B:11-90
1j	d1cvjb2	B:91-175
1k	d1cvjc1	C:11-90
1l	d1cvjc2	C:91-178
1m	d1cvjd1	D:11-90
1n	d1cvjd2	D:91-175
1o	d1cvje1	E:11-90
1p	d1cvje2	E:91-178

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

[unclassified] (45)

1a	1cvjG02	G:88-175
1b	1cvjC02	C:88-178
1c	1cvjE02	E:88-178
1d	1cvjA02	A:88-179
1e	1cvjD02	D:88-174
1f	1cvjB02	B:88-173
1g	1cvjF02	F:88-170
1h	1cvjA01	A:11-87
1i	1cvjB01	B:11-87
1j	1cvjC01	C:11-87
1k	1cvjD01	D:11-87
1l	1cvjE01	E:11-87
1m	1cvjF01	F:11-87
1n	1cvjG01	G:11-87
1o	1cvjH01	H:11-87
1p	1cvjH02	H:88-152

(no "Pfam Domain" information available for 1CVJ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (PABP1_HUMAN | P11940)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0008143	poly(A) binding	Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
	GO:0008266	poly(U) RNA binding	Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0008494	translation activator activity	Any of a group of soluble proteins functioning in the activation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0048255	mRNA stabilization	Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
	GO:2000623	negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay.
	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:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
	GO:0060213	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0045070	positive regulation of viral genome replication	Any process that activates or increases the frequency, rate or extent of viral genome replication.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0036464	cytoplasmic ribonucleoprotein granule	A ribonucleoprotein granule located in the cytoplasm.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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	1cvj
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(no "Related Entries Specified in the PDB File" available for 1CVJ)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (4, 32)

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