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Title :   X-RAY CRYSTAL STRUCTURE OF MAGI-1 PDZ1 BOUND TO THE C-TERMINAL PEPTIDE OF HPV18 E6

Authors :   X. S. Chen, Y. Zhang, J. Dasgupta, L. Banks, M. Thomas

Date :   09 Aug 06 (Deposition) - 20 Feb 07 (Release) - 23 Sep 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Pdz, E6 Binding, Tumor Suppressor, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhang, J. Dasgupta, R. Z. Ma, L. Banks, M. Thomas, X. S. Chen
Structures Of A Human Papillomavirus (Hpv) E6 Polypeptide Bound To Maguk Proteins: Mechanisms Of Targeting Tumor Suppressors By A High-Risk Hpv Oncoprotein.
J. Virol. V. 81 3618 2007
PubMed-ID: 17267502 | Reference-DOI: 10.1128/JVI.02044-06
(for further references see the PDB file header)

Molecule 1 - MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	XA90
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ1 DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	BAI1-ASSOCIATED PROTEIN 1, BAP-1, MEMBRANE- ASSOCIATED GUANYLATE KINASE INVERTED 1, MAGI-1

Molecule 2 - PEPTIDE E6
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THE SEQUENCE OF THIS PEPTIDE CAN BE FOUND IN HUMAN PAPILLOMAVIRUS TYPE 18 (VIRUS)
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:456 , SER B:458 , SER B:459	BINDING SITE FOR RESIDUE SO4 B 900
2	AC2	SOFTWARE	ARG A:456 , SER A:458 , SER A:459 , ILE A:524 , HOH A:2070 , HOH D:2107	BINDING SITE FOR RESIDUE SO4 A 901

Asymmetric/Biological Unit

No.	Residues
1	A:506	-	B:533
2	A:533	-	B:506

(no "Cis Peptide Bond" information available for 2I04)

(no "SAP(SNP)/Variant" information available for 2I04)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAGI1_MOUSE	17-105 464-533 635-713 833-915 990-1074 1132-1214	2	- A:452-521 B:452-521 - - - -

(no "Exon" information available for 2I04)

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:85
 aligned with MAGI1_MOUSE | Q6RHR9 from UniProtKB/Swiss-Prot  Length:1471

    Alignment length:91
                                   465       475       485       495       505       515       525       535       545 
         MAGI1_MOUSE    456 SELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCR  546
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------eeeeee.......eeeee.......eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: A:452-521 UniProt: 464-533                                  ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                2i04 A  450 S------IHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCR  534
                            |      453       463       473       483       493       503       513       523       533 
                            |    451                                                                                   
                          450

Chain B from PDB  Type:PROTEIN  Length:85
 aligned with MAGI1_MOUSE | Q6RHR9 from UniProtKB/Swiss-Prot  Length:1471

    Alignment length:91
                                   465       475       485       495       505       515       525       535       545 
         MAGI1_MOUSE    456 SELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCR  546
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------eeeeee.......eeeee.......eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: B:452-521 UniProt: 464-533                                  ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                2i04 B  450 S------IHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCR  534
                            |      453       463       473       483       493       503       513       523       533 
                          450    451

Chain C from PDB  Type:PROTEIN  Length:5
 aligned with VE6_HPV18 | P06463 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:5
           VE6_HPV18    154 RETQV  158
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                2i04 C 2002 RETQV 2006

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with VE6_HPV18 | P06463 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:7
           VE6_HPV18    152 RRRETQV  158
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...eeee Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                2i04 D 2000 RRRETQV 2006

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 2I04)

(no "CATH Domain" information available for 2I04)

(no "Pfam Domain" information available for 2I04)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MAGI1_MOUSE | Q6RHR9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0051393	alpha-actinin binding	Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats.
	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).
	GO:0032947	protein complex scaffold activity	A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
	GO:0070997	neuron death	The process of cell death in a neuron.
cellular component
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D (VE6_HPV18 | P06463)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039586	modulation by virus of host PP1 activity	The process in which a virus effects a change in host protein phosphatase-1 (PP1) activity, a serine/threonine phosphatase. Different viruses modulate host PP1 activity to remove phosphates from various cellular substrates and downregulate the host's antiviral response.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0039548	suppression by virus of host IRF3 activity	Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
	GO:0039574	suppression by virus of host TYK2 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host TYK2 (tyrosine kinase 2) activity. TYK2 is an intracellular signal-transducing tyrosine kinase that associates with the cytoplasmic tails of cytokine receptors and transmits the cytokine signal by phosphorylating receptor subunits.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	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:0044204	host cell nuclear matrix	The dense fibrillar network lying on the inner side of the host nuclear membrane.
	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.

Asymmetric/Biological Unit
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	VE6_HPV18 \| P06463
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	VE6_HPV18 \| P06463	:	2i0i 2i0l 4jor

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Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (2, 2)

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