1XYH - JenaLib

Title :   CRYSTAL STRUCTURE OF RECOMBINANT HUMAN CYCLOPHILIN J

Authors :   L. -L. Huang, X. -M. Zhao, C. -Q. Huang, L. Yu, Z. -X. Xia

Date :   10 Nov 04 (Deposition) - 15 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A

Keywords :   Cyclophilin J, Beta-Barrel, Helix, Disulfide Bridge, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. L. Huang, X. M. Zhao, C. Q. Huang, L. Yu, Z. X. Xia
Structure Of Recombinant Human Cyclophilin J, A Novel Member Of The Cyclophilin Family.
Acta Crystallogr. , Sect. D V. 61 316 2005
PubMed-ID: 15735342 | Reference-DOI: 10.1107/S0907444904033189
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (6, 6)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1h	ENST00000392283	1h	ENSE00001844706	chr2:201753877-201753679	199	PPIL3_HUMAN	-	0	0	-	-
1.3c	ENST00000392283	3c	ENSE00002195284	chr2:201752408-201752336	73	PPIL3_HUMAN	1-1	1	1	A:1-1	1
1.5a	ENST00000392283	5a	ENSE00002036206	chr2:201750495-201750421	75	PPIL3_HUMAN	2-26	25	1	A:2-26	25
1.6a	ENST00000392283	6a	ENSE00002072364	chr2:201747158-201747065	94	PPIL3_HUMAN	27-58	32	1	A:27-58	32
1.7c	ENST00000392283	7c	ENSE00002167871	chr2:201746211-201746144	68	PPIL3_HUMAN	58-80	23	1	A:58-80	23
1.9c	ENST00000392283	9c	ENSE00002084627	chr2:201741760-201741642	119	PPIL3_HUMAN	81-120	40	1	A:81-120	40
1.10h	ENST00000392283	10h	ENSE00001922818	chr2:201736244-201735679	566	PPIL3_HUMAN	120-161	42	1	A:120-160	41

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:160
 aligned with PPIL3_HUMAN | Q9H2H8 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
          PPIL3_HUMAN     1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPFA 160
               SCOP domains d1xyha1 A:1-160 Cyclophilin-like protein PPIL3B                                                                                                                  SCOP domains
               CATH domains 1xyhA00 A:1-160 Cyclophilin                                                                                                                                      CATH domains
               Pfam domains -Pro_isomerase-1xyhA01 A:2-154                                                                                                                            ------ Pfam domains
         Sec.struct. author eeeeee....eeeeeehhhhhhhhhhhhhhhhhh....eeeeeeee..eeeee...............................eeeeee.........eeeeee..hhhhh...eeeeeeeehhhhhhhhhhh............eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------E-------------- SAPs(SNPs)
                PROSITE (1) -----CSA_PPIASE_2  PDB: A:6-154 UniProt: 6-154                                                                                                            ------ PROSITE (1)
                PROSITE (2) ------------------------------------CSA_PPIASE_1      ---------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1Exon 1.5a  PDB: A:2-26   Exon 1.6a  PDB: A:27-58         -------------------------------------------------------------Exon 1.10h  PDB: A:120-160 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.7c  PDB: A:58-80Exon 1.9c  PDB: A:81-120 UniProt: 81-120---------------------------------------- Transcript 1 (2)
                 1xyh A   1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPFA 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PPIL3_HUMAN | Q9H2H8)

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: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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1xyh)

	Sites
(no "Sites" information available for 1xyh)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xyh)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1xyh
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PPIL3_HUMAN \| Q9H2H8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	5.2.1.8
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PPIL3_HUMAN \| Q9H2H8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description