2X7K - JenaLib

Title :   THE CRYSTAL STRUCTURE OF PPIL1 IN COMPLEX WITH CYCLOSPORINE A SUGGESTS A BINDING MODE FOR SKIP

Authors :   C. M. Stegmann, R. Luehrmann, M. C. Wahl

Date :   01 Mar 10 (Deposition) - 23 Mar 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

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

Keywords :   Isomerase-Immunosuppressant Complex, Isomerase-Cyclosporin Complex, Cyclosporin A, Immunosuppressant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Stegmann, R. Luehrmann, M. C. Wahl
The Crystal Structure Of Ppil1 Bound To Cyclosporine A Suggests A Binding Mode For A Linear Epitope Of The Skip Protein.
Plos One V. 5 13 2010
PubMed-ID: 20368803 | Reference-DOI: 10.1371/JOURNAL.PONE.0010013

Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 1
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6-P1-PPIL1
	Expression System Strain	:	ROSETTA2
	Expression System Taxid	:	562
	Expression System Variant	:	DE3
	Expression System Vector	:	PGEX-6-P1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PPIASE, ROTAMASE, PPIL1

Molecule 2 - CYCLOSPORIN A
	Chains	:	B
	Organism Scientific	:	TOLYPOCLADIUM INFLATUM
	Organism Taxid	:	29910
	Synonym	:	CICLOSPORIN, CICLOSPORINE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 12)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:31 , ASP A:89 , CYS A:133 , HOH A:2087 , HOH A:2190	BINDING SITE FOR RESIDUE CD A1167
2	AC2	SOFTWARE	GLU A:26 , HIS A:87 , CYS A:133 , HOH A:2239	BINDING SITE FOR RESIDUE CD A1168
3	AC3	SOFTWARE	ASP A:7 , HOH A:2267	BINDING SITE FOR RESIDUE NA A1169
4	AC4	SOFTWARE	GLU A:17 , ARG A:55 , PHE A:60 , GLN A:63 , GLY A:71 , ALA A:101 , ASN A:102 , GLN A:111 , PHE A:113 , TRP A:121 , HIS A:126 , MET A:144 , HOH A:2032 , HOH A:2033 , HOH A:2066 , HOH A:2137 , HOH A:2161 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2007 , HOH B:2008	BINDING SITE FOR CHAIN B OF CYCLOSPORIN A

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (4, 4)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:164
 aligned with PPIL1_HUMAN | Q9Y3C6 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:164
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162    
          PPIL1_HUMAN     3 AIPPDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG 166
               SCOP domains d2x7ka_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Pro_isomerase-2x7kA01 A:13-163                                                                                                                         --- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeee....hhhhhhhhhhhhhhh....ee..eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhh..............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------S---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------CSA_PPIASE_2  PDB: A:17-164 UniProt: 17-164                                                                                                         -- PROSITE (1)
                PROSITE (2) ---------------------------------------------CSA_PPIASE_1      ----------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1         ---------------------------------------------------Exon 1.4  PDB: A:71-94  ------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.2  PDB: A:19-71 UniProt: 19-71                ----------------------Exon 1.5  PDB: A:94-166 UniProt: 94-166                                   Transcript 1 (2)
                 2x7k A   3 AIPPDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG 166
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 2x7k B   1 xxxxxxxxVxA  11
                            ||||||||10 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
                                    10-MLE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PPIL1_HUMAN | Q9Y3C6)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO: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: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:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000413	protein peptidyl-prolyl isomerization	The modification of a protein by cis-trans isomerization of a proline residue.
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: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: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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	2x7k
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1bck	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN C
1c5f	CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A
1csa	SOLUTION STRUCTURE OF E.COLI CYCLOPHILIN (F112W) COMPLEXED WITH CYCLOSPORIN A
1cwa	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
1cwb	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 5
1cwc	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwf	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN D
1cwh	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A MODIFIED AT POSITION 7
1cwi	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITION 7
1cwj	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITIONS 5 AND 7.
1cwk	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITIONS 5 AND 7.
1cwl	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwm	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwo	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH NODIFIED CYCLOSPORIN C AT POSITIONS 1, AND 9
1cya	SOLUTION STRUCTURE OF HUMAN CYCLOPHILIN COMPLEXED WIYH CYCLOSPORIN A
1cyb	SOLUTION STRUCTURE OF HUMAN CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1cyn	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN B COMPLEXED WITH MODIFIED CYCLOSPORIN A
1ikf	CRYSTAL STRUCTURE OF CTCLOSPORIN-FAB COMPLEX
1m63	CRYSTAL STRUCTURE OF CALCINEURIN-CYCLOPHILIN-CYCLOSPORIN COMPLEX
1mf8	CRYSTAL STRUCTURE OF HUMAN CALCINEURIN COMPLEXED WITH HUMAN CYCLOPHILIN AND CYCLOSPORIN A
1mik	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 6
1qng	CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1qnh	CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM CYCLOPHILIN (DOUBLE MUTANT) COMPLEXED WITH CYCLOSPORIN A
1xq7	CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1xwn	SOLUTION STRUCTURE OF CYCLOPHILIN LIKE 1(PPIL1) AND INSIGHTS INTO ITS INTERACTION WITH SKIP
2esl	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
2oju	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN J COMPLEXED WITH CYCLOSPORIN A
2poy	CRYSTAL STRUCTURE OF CRYPTOSPORIDIUM PARVUM IOWA II CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
2rma	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
2rmb	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 5
2rmc	CRYSTAL STRUCTURE OF MURINE CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
2wfj	CRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF HUMAN CYCLOPHILIN G COMPLEXED WITH CYCLOSPORIN A
2x2c	CRYSTAL STRUCTURE OF HUMAN ACETYL-CYPA COMPLEXED WITH CYCLOSPORINE A
2z6w	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN D IN COMPLEX WITH CYCLOSPORIN A
3bo7	CRYSTAL STRUCTURE OF CYCLOSPHILIN A FROM TOXOPLASMA GONDII COMPLEXED WIT CYCLOSPORIN A
3cys	SOLUTION STRUCTURE OF THE HUMAN CYCLOSPORIN A COMPLEXED WITH CYCLOSPORIN A
3eov	CRYSTAL STRUCTURE OF CYCLOPHILIN FROM LEISHMANIA DONOVANI COMPLEXED WITH CYCLOSPORIN A

Description