3RK6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MIDDLE DOMAIN OF HUMAN PAIP1

Authors :   J. Lei, J. R. Mesters, R. Hilgenfeld

Date :   17 Apr 11 (Deposition) - 18 May 11 (Release) - 08 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Heat Fold, Pabp, Eif4A, Eif3, Translation Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lei, J. R. Mesters, A. Brunn, R. Hilgenfeld
Crystal Structure Of The Middle Domain Of Human Poly(A)-Binding Protein-Interacting Protein 1.
Biochem. Biophys. Res. Commun. V. 408 680 2011
PubMed-ID: 21539810 | Reference-DOI: 10.1016/J.BBRC.2011.04.088

Molecule 1 - POLYADENYLATE-BINDING PROTEIN-INTERACTING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	MIDDLE DOMAIN (MIF4G, UNP RESIDUES 157-373)
	Gene	:	PAIP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PAIP-1, PABP-INTERACTING PROTEIN 1, POLY(A)-BINDING PROTEIN- INTERACTING PROTEIN 1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3RK6)

(no "Site" information available for 3RK6)

(no "SS Bond" information available for 3RK6)

(no "Cis Peptide Bond" information available for 3RK6)

(no "SAP(SNP)/Variant" information available for 3RK6)

(no "PROSITE Motif" information available for 3RK6)

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000306846	2b	ENSE00002201985	chr5:43557181-43556684	498	PAIP1_HUMAN	1-89	89	0	-	-
1.4a	ENST00000306846	4a	ENSE00001687835	chr5:43556101-43555932	170	PAIP1_HUMAN	89-145	57	0	-	-
1.5	ENST00000306846	5	ENSE00002199905	chr5:43548015-43547830	186	PAIP1_HUMAN	146-207	62	2	A:78-128 B:78-128	51 51
1.6b	ENST00000306846	6b	ENSE00001175015	chr5:43543218-43543106	113	PAIP1_HUMAN	208-245	38	2	A:129-166 B:129-166	38 38
1.7b	ENST00000306846	7b	ENSE00001175008	chr5:43539137-43539026	112	PAIP1_HUMAN	245-282	38	2	A:166-203 B:166-203	38 38
1.8b	ENST00000306846	8b	ENSE00001174998	chr5:43537046-43536921	126	PAIP1_HUMAN	283-324	42	2	A:204-245 B:204-245	42 42
1.9	ENST00000306846	9	ENSE00001174992	chr5:43535742-43535636	107	PAIP1_HUMAN	325-360	36	2	A:246-281 B:246-281	36 36
1.10	ENST00000306846	10	ENSE00001174982	chr5:43535072-43534955	118	PAIP1_HUMAN	360-399	40	2	A:281-294 B:281-294	14 14
1.11	ENST00000306846	11	ENSE00001174974	chr5:43533894-43533840	55	PAIP1_HUMAN	400-418	19	0	-	-
1.12b	ENST00000306846	12b	ENSE00001174964	chr5:43529981-43529888	94	PAIP1_HUMAN	418-449	32	0	-	-
1.13f	ENST00000306846	13f	ENSE00001148824	chr5:43527571-43526369	1203	PAIP1_HUMAN	449-479	31	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:217
 aligned with PAIP1_HUMAN | Q9H074 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:217
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       
          PAIP1_HUMAN   157 TLSEYVQDFLNHLTEQPGSFETEIEQFAETLNGCVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELR 373
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee.....ee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:78-128 UniProt: 146-207           Exon 1.6b  PDB: A:129-166             -------------------------------------Exon 1.8b  PDB: A:204-245 UniProt: 283-324-----------------------------------Exon 1.10      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.7b  PDB: A:166-203             ------------------------------------------Exon 1.9  PDB: A:246-281            ------------- Transcript 1 (2)
                 3rk6 A  78 TLSEYVQDFLNHLTEQPGSFETEIEQFAETLNGCVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELR 294
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with PAIP1_HUMAN | Q9H074 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:217
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       
          PAIP1_HUMAN   157 TLSEYVQDFLNHLTEQPGSFETEIEQFAETLNGCVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELR 373
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --MIF4G-3rk6B01 B:80-294                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) --MIF4G-3rk6B02 B:80-294                                                                                                                                                                                                  Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee.....ee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:78-128 UniProt: 146-207           Exon 1.6b  PDB: B:129-166             -------------------------------------Exon 1.8b  PDB: B:204-245 UniProt: 283-324-----------------------------------Exon 1.10      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.7b  PDB: B:166-203             ------------------------------------------Exon 1.9  PDB: B:246-281            ------------- Transcript 1 (2)
                 3rk6 B  78 TLSEYVQDFLNHLTEQPGSFETEIEQFAETLNGCVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELR 294
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287

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 3RK6)

(no "CATH Domain" information available for 3RK6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TPR (230)

Family: MIF4G (5)

Homo sapiens (Human) (3)

1a	MIF4G-3rk6B01	B:80-294
1b	MIF4G-3rk6B02	B:80-294

Asymmetric Unit(hide GO term definitions)

Chain A,B (PAIP1_HUMAN | Q9H074)

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: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: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: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: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:0006417	regulation of translation	Any process that modulates 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: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: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.

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Biological Units
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	3rk6
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	PAIP1_HUMAN \| Q9H074	:	1jh4 3ntw

(no "Related Entries Specified in the PDB File" available for 3RK6)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (6, 12)

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