4DGB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   TRIMCYP CYCLOPHILIN DOMAIN FROM MACACA MULATTA: HIV-2 CA CYCLOPHILIN-BINDING LOOP COMPLEX

Authors :   M. E. C. Caines, K. Bichel, A. J. Price, W. A. Mcewan, L. C. James

Date :   25 Jan 12 (Deposition) - 08 Feb 12 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Anti-Viral Protein, Isomerase-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Caines, K. Bichel, A. J. Price, W. A. Mcewan, G. J. Towers, B. J. Willett, S. M. Freund, L. C. James
Diverse Hiv Viruses Are Targeted By A Conformationally Dynamic Antiviral.
Nat. Struct. Mol. Biol. V. 19 411 2012
PubMed-ID: 22407016 | Reference-DOI: 10.1038/NSMB.2253

Molecule 1 - TRIMCYP
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POPT
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CYCLOPHILIN DOMAIN (UNP RESIDUES 304-468)
	Gene	:	TRIMCYP
	Organism Common	:	RHESUS MACAQUE
	Organism Scientific	:	MACACA MULATTA
	Organism Taxid	:	9544
	Synonym	:	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE

Molecule 2 - CAPSID PROTEIN
	Chains	:	B
	Engineered	:	YES
	Fragment	:	CYCLOPHILIN-BINDING LOOP (UNP RESIDUES 221-226)
	Organism Common	:	HIV-2
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 2
	Organism Taxid	:	11720
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4DGB)

(no "Site" information available for 4DGB)

(no "SS Bond" information available for 4DGB)

(no "Cis Peptide Bond" information available for 4DGB)

(no "SAP(SNP)/Variant" information available for 4DGB)

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:121-164	44

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:163
 aligned with B0LJC8_MACMU | B0LJC8 from UniProtKB/TrEMBL  Length:468

    Alignment length:163
                                   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464   
         B0LJC8_MACMU   305 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL 467
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...........eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dgb A   2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain A from PDB  Type:PROTEIN  Length:163
 aligned with PPIA_MACMU | P62940 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
           PPIA_MACMU     2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL 164
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...........eeeeeeeee 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:121-164 UniProt: 121-165    Transcript 1 (2)
                 4dgb A   2 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:6
 aligned with GAG_HV2RO | P04590 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:6
            GAG_HV2RO   221 PGPLPA 226
               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
                 4dgb B  86 PGPLPA  91

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 4DGB)

(no "CATH Domain" information available for 4DGB)

(no "Pfam Domain" information available for 4DGB)

Asymmetric/Biological Unit(hide GO term definitions)

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.

Chain A (B0LJC8_MACMU | B0LJC8)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain B (GAG_HV2RO | P04590)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0046755	viral budding	A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
	GO:0039702	viral budding via host ESCRT complex	Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0072494	host multivesicular body	A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019013	viral nucleocapsid	The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric/Biological Unit
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	4dgb
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	B0LJC8_MACMU \| B0LJC8
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	GAG_HV2RO \| P04590
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	PPIA_MACMU \| P62940
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	5.2.1.8
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	PPIA_MACMU \| P62940
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UniProtKB/Swiss-Prot
	B0LJC8_MACMU \| B0LJC8	:	4dga 4dgc 4dgd 4dge
	GAG_HV2RO \| P04590	:	2wlv
	PPIA_MACMU \| P62940	:	1cwa 1cwb 1cwc 1cwj 1cwk 1cwl 1mik 1rmh 1vbs 1vbt 2cyh 2wlw 3cyh 3cys 4cyh 4dga 4dgc 4dgd 4dge 5cyh

4dga	TRIMCYP CYCLOPHILIN DOMAIN FROM MACACA MULATTA: HIV-1 CA(O- LOOP) COMPLEX
4dgc	TRIMCYP CYCLOPHILIN DOMAIN FROM MACACA MULATTA: CYCLOSPORIN A COMPLEX
4dgd	TRIMCYP CYCLOPHILIN DOMAIN FROM MACACA MULATTA: H70C MUTANT
4dge	TRIMCYP CYCLOPHILIN DOMAIN FROM MACACA MULATTA: H70C MUTANT, HIV-1 CA(O-LOOP) COMPLEX

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Ligands, Modified Residues, Ions (0, 0)

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PROSITE Motifs (2, 2)

Exons (5, 5)

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (37, 43)

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