2WLW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE N-TERMINAL CAPSID DOMAIN OF HIV-2

Authors :   A. J. Price, F. Marzetta, M. Lammers, L. M. J. Ylinen, T. Schaller, S. J. Wilson, G. J. Towers, L. C. James

Date :   26 Jun 09 (Deposition) - 22 Sep 09 (Release) - 06 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Rotamase, Isomerase, Rhesus Macaque Trim-Cyp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Price, F. Marzetta, M. Lammers, L. M. J. Ylinen, T. Schaller, S. J. Wilson, G. J. Towers, L. C. James
Active Site Remodelling Switches Hiv Specificity Of Antiretroviral Trimcyp
Nat. Struct. Mol. Biol. V. 16 1036 2009
PubMed-ID: 19767750 | Reference-DOI: 10.1038/NSMB.1667

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CYPA DOMAIN, RESIDUES 46-210
	Organism Scientific	:	MACACA MULATTA
	Organism Taxid	:	9544
	Synonym	:	TRIM-CYP

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2WLW)

(no "Site" information available for 2WLW)

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

(no "Cis Peptide Bond" information available for 2WLW)

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	PPIA_MACMU	7-163	1	A:7-163
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	PPIA_MACMU	48-65	1	A:48-65

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSMMUT00000023383	1	ENSMMUE00000161287	chr3:81547389-81547272	118	PPIA_MACMU	1-23	23	1	A:2-23	22
1.2	ENSMMUT00000023383	2	ENSMMUE00000161290	chr3:81544822-81544792	31	PPIA_MACMU	24-34	11	1	A:24-34	11
1.3	ENSMMUT00000023383	3	ENSMMUE00000161294	chr3:81544663-81544575	89	PPIA_MACMU	34-63	30	1	A:34-63	30
1.4	ENSMMUT00000023383	4	ENSMMUE00000161297	chr3:81544363-81544191	173	PPIA_MACMU	64-121	58	1	A:64-121	58
1.5	ENSMMUT00000023383	5	ENSMMUE00000161300	chr3:81543093-81542746	348	PPIA_MACMU	121-165	45	1	A:121-165	45

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 B1P761_MACMU | B1P761 from UniProtKB/TrEMBL  Length:210

    Alignment length:164
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    
         B1P761_MACMU    47 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE 210
               SCOP domains d2wlwa_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Pro_isomerase-2wlwA01 A:7-163                                                                                                                                -- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...........eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wlw A   2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain A from PDB  Type:PROTEIN  Length:164
 aligned with PPIA_MACMU | P62940 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           PPIA_MACMU     2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE 165
               SCOP domains d2wlwa_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Pro_isomerase-2wlwA01 A:7-163                                                                                                                                -- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...........eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CSA_PPIASE_2  PDB: A:7-163 UniProt: 7-163                                                                                                                    -- PROSITE (1)
                PROSITE (2) ----------------------------------------------CSA_PPIASE_1      ---------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:2-23 Exon 1.2   -----------------------------Exon 1.4  PDB: A:64-121 UniProt: 64-121                   -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.3  PDB: A:34-63        ---------------------------------------------------------Exon 1.5  PDB: A:121-165 UniProt: 121-165     Transcript 1 (2)
                 2wlw A   2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cyclophilin-like (169)

Superfamily: Cyclophilin-like (169)

Family: Cyclophilin (peptidylprolyl isomerase) (160)

Protein domain: automated matches (38)

Rhesus monkey (Macaca mulatta) [TaxId: 9544] (4)

d2wlwa_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cyclophil-like (65)

Family: Pro_isomerase (53)

Macaca mulatta (Rhesus macaque) (1)

Pro_isomerase-2wlwA01

A:7-163

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (B1P761_MACMU | B1P761)

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).
biological process
	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.

Chain A (PPIA_MACMU | P62940)

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:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
biological process
	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.
	GO:0045069	regulation of viral genome replication	Any process that modulates the frequency, rate or extent of viral genome replication.
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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	2wlw
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2wlv	STRUCTURE OF THE N-TERMINAL CAPSID DOMAIN OF HIV-2

Description

Compounds

Structural Features

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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)

PROSITE Motifs (2, 2)

Exons (5, 5)

Sequences/Alignments

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SCOP Domains (1, 1)

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