3J4P - JenaLib

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Title :   ELECTRON MICROSCOPY ANALYSIS OF A DISACCHARIDE ANALOG COMPLEX REVEALS RECEPTOR INTERACTIONS OF ADENO-ASSOCIATED VIRUS

Authors :   Q. Xie, M. S. Chapman

Date :   10 Sep 13 (Deposition) - 16 Oct 13 (Release) - 20 Nov 13 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   4.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (60x)

Keywords :   Virus Cell-Receptor Interaction, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Xie, M. Spilman, N. L. Meyer, T. F. Lerch, S. M. Stagg, M. S. Chapman
Electron Microscopy Analysis Of A Disaccharide Analog Complex Reveals Receptor Interactions Of Adeno-Associated Virus.
J. Struct. Biol. V. 184 129 2013
PubMed-ID: 24036405 | Reference-DOI: 10.1016/J.JSB.2013.09.004

Molecule 1 - CAPSID PROTEIN VP1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PAVDJ
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	SEE REMARK 999
	Gene	:	CAP
	Organism Scientific	:	ADENO-ASSOCIATED VIRUS
	Organism Taxid	:	272636

		1
Asymmetric Unit	:	A
Biological Unit 1 (60x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	NA	1	Ligand/Ion	SODIUM ION
3	SCR	1	Ligand/Ion	SUCROSE OCTASULFATE

Biological Unit 1 (1, 60)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	SCR	60	Ligand/Ion	SUCROSE OCTASULFATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:585 , ARG A:587 , ARG A:590 , NA A:802 , MG A:803	BINDING SITE FOR RESIDUE SCR A 801
2	AC2	SOFTWARE	SCR A:801	BINDING SITE FOR RESIDUE NA A 802
3	AC3	SOFTWARE	SCR A:801	BINDING SITE FOR RESIDUE MG A 803

(no "SS Bond" information available for 3J4P)

Asymmetric Unit

No.	Residues
1	Asn A:520	-	Pro A:521

(no "SAP(SNP)/Variant" information available for 3J4P)

(no "PROSITE Motif" information available for 3J4P)

(no "Exon" information available for 3J4P)

Asymmetric 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:517
 aligned with CAPSD_AAV2S | P03135 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:517
                                                                        265                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                     264  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                   230       240       250       260   |  |268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       
          CAPSD_AAV2S   221 VGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISSQS--GASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL 735
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................ee..eeeee.........ee..............eeeeeeeee..........hhhhhhhhhhheeeeeeeeeeeeee....eeeeee..eeee......eeeeee.........................ee..eeeeee..............hhhhh..eeee....eeeeee......ee..ee................eeeeeee........eeeeeee.............ee.......eee.................ee......ee................eee.....eee.............eee.................eeee...........eeee........ee........................................eeeee.....................eeeeeeee.eeeeeeee...........................................ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j4p A 221 VGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISNSTSGGSSNDNAYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFTYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTQTTGGTTNTQTLGFSQGGPNTMANQAKNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQSKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL 737
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730

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 3J4P)

(no "CATH Domain" information available for 3J4P)

(no "Pfam Domain" information available for 3J4P)

Asymmetric Unit(hide GO term definitions)

Chain A (CAPSD_AAV2S | P03135)

molecular function
	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.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0039665	permeabilization of host organelle membrane involved in viral entry into host cell	Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	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:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0039615	T=1 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=1 symmetry. The T=1 capsid is composed of 12 pentameric capsomeres.
	GO:0044196	host cell nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic host cells.
	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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:520 - Pro A:521	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3j4p
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	CAPSD_AAV2S \| P03135	:	1lp3 3j1s 5ipi 5ipk

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (0, 0)

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