4B4N - JenaLib

Title :   CPSF6 DEFINES A CONSERVED CAPSID INTERFACE THAT MODULATES HIV-1 REPLICATION

Authors :   A. J. Price, L. C. James

Date :   31 Jul 12 (Deposition) - 19 Sep 12 (Release) - 19 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

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

Keywords :   Viral Protein-Rna Binding Protein Complex, Hiv-1, Cyclophilin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Price, A. J. Fletcher, T. Schaller, T. Elliott, K. Lee, V. N. Kewalramani, J. W. Chin, G. J. Towers, L. C. James
Cpsf6 Defines A Conserved Capsid Interface That Modulates Hiv-1 Replication.
Plos Pathog. V. 8 2896 2012
PubMed-ID: 22956906 | Reference-DOI: 10.1371/JOURNAL.PPAT.1002896

Compounds

Molecule 1 - GAG PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Taxid	:	4932
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 33-178
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

Molecule 2 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
	Chains	:	B
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Taxid	:	4932
	Fragment	:	RESIDUES 313-327
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CPSF6, CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 68 KDA SUBUNIT, CFIM68, CPSF 68 KDA SUBUNIT, PRE-MRNA CLEAVAGE FACTOR IM 68 KDA SUBUNIT, PROTEIN HPBRII-4/7

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:136
 aligned with A9PKC6_9HIV1 | A9PKC6 from UniProtKB/TrEMBL  Length:276

    Alignment length:146
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172      
         A9PKC6_9HIV1    33 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS 178
               SCOP domains d4b4na_ A: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...----------...hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b4n A   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPV----------REPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS 146
                                    10        20        30        40        50        60        70        80     |   -      |100       110       120       130       140      
                                                                                                                86         97

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with CPSF6_HUMAN | Q16630 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:15
                                   285     
          CPSF6_HUMAN   276 PVLFPGQPFGQPPLG 290
               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
                 4b4n B 322 PVLFPGQPFGQPPLG 336
                                   331

Legend:		→ Mismatch	(orange background)
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	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 (0, 0)

Gene Ontology (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A9PKC6_9HIV1 | A9PKC6)

biological 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.
cellular component
	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:0019012	virion	The complete fully infectious extracellular virus particle.

Chain B (CPSF6_HUMAN | Q16630)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	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:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005849	mRNA cleavage factor complex	Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.
	GO:0042382	paraspeckles	Discrete subnuclear bodies in the interchromatin nucleoplasmic space, often located adjacent to nuclear specks. 10-20 paraspeckles are typically found in human cell nuclei.

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		Asn A:121 - Pro A:122	[ RasMol ]

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Description