1X9P - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PENTON BASE

Authors :   C. Zubieta, G. Schoehn, J. Chroboczek, S. Cusack

Date :   24 Aug 04 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Jellyroll Domain, Anti-Parallel Beta Sheet, Insertion Domain, Virus Like Particle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Zubieta, G. Schoehn, J. Chroboczek, S. Cusack
The Structure Of The Human Adenovirus 2 Penton
Mol. Cell V. 17 121 2005
PubMed-ID: 15629723 | Reference-DOI: 10.1016/J.MOLCEL.2004.11.041
(for further references see the PDB file header)

Molecule 1 - PENTON PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	HTB
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RESIDUES 49-571
	Gene	:	PENTON BASE
	Organism Scientific	:	HUMAN ADENOVIRUS 2
	Organism Taxid	:	10515
	Synonym	:	VIRION COMPONENT III, PENTON BASE PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	C15	2	Ligand/Ion	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 180)

No.	Name	Count	Type	Full Name
1	C15	120	Ligand/Ion	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
2	SO4	60	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:86 , LEU A:92 , ARG A:540	BINDING SITE FOR RESIDUE SO4 A 700
2	AC2	SOFTWARE	ARG A:146 , TRP A:165 , ARG A:272 , ASP A:276	BINDING SITE FOR RESIDUE C15 A 998
3	AC3	SOFTWARE	LYS A:263 , GLY A:270 , PHE A:271 , ARG A:272 , TRP A:422	BINDING SITE FOR RESIDUE C15 A 999

(no "SS Bond" information available for 1X9P)

(no "Cis Peptide Bond" information available for 1X9P)

(no "SAP(SNP)/Variant" information available for 1X9P)

(no "PROSITE Motif" information available for 1X9P)

(no "Exon" information available for 1X9P)

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:460
 aligned with CAPSP_ADE02 | P03276 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:521
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       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 
          CAPSP_ADE02    49 TGGRNSIRYSELAPLFDTTRVYLVDNKSTDVASLNYQNDHSNFLTTVIQNNDYSPGEASTQTINLDDRSHWGGDLKTILHTNMPNVNEFMFTNKFKARVMVSRSLTKDKQVELKYEWVEFTLPEGNYSETMTIDLMNNAIVEHYLKVGRQNGVLESDIGVKFDTRNFRLGFDPVTGLVMPGVYTNEAFHPDIILLPGCGVDFTHSRLSNLLGIRKRQPFQEGFRITYDDLEGGNIPALLDVDAYQASLKDDTEQGGDGAGGGNNSGSGAEENSNAAAAAMQPVEDMNDHAIRGDTFATRAEEKRAEAEAAAEAAAPAAQPEVEKPQKKPVIKPLTEDSKKRSYNLISNDSTFTQYRSWYLAYNYGDPQTGIRSWTLLCTPDVTCGSEQVYWSLPDMMQDPVTFRSTSQISNFPVVGAELLPVHSKSFYNDQAVYSQLIRQFTSLTHVFNRFPENQILARPPAPTITTVSENVPALTDHGTLPLRNSIGGVQRVTITDARRRTCPYVYKALGIVSPRVLSSR 569
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x9pA01 A:49-130,A:436-467,A:521-569 Penton protein; domain 1                     1x9pA02 A:131-435,A:468-520 adenovirus 2 penton base, domain 2                                                                                                                                                                                                                                                   1x9pA01 Penton protein; domain 11x9pA02 A:131-435,A:468-520                          1x9pA01 A:49-130,A:436-467,A:521-569              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee............eeee..hhhhhhhh.......eeeee.......hhhhhh..eeee...eeeeeeeeeeeee............eeeeeeeeeee.......eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh......hhhhh............ee....ee..............ee....eee....hhhhhhheee........eee.hhh...eee...hhhhhhhh...---------------------------------------------.............----------------...........ee...ee.........eeeeeehhhhhhhh....hhhhheee..........eeee................hhhhh...eeee..eeeeee..hhhhhhhhh...........................eeeeee..eeeeeeeeee..eee.eeeee.ee........eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9p A  49 TGGRNSIRYSELAPLFDTTRVYLVDNKSTDVASLNYQNDHSNFLTTVIQNNDYSPGEASTQTINLDDRSHWGGDLKTILHTNMPNVNEFMFTNKFKARVMVSRSLTKDKQVELKYEWVEFTLPEGNYSETMTIDLMNNAIVEHYLKVGRQNGVLESDIGVKFDTRNFRLGFDPVTGLVMPGVYTNEAFHPDIILLPGCGVDFTHSRLSNLLGIRKRQPFQEGFRITYDDLEGGNIPALLDVDAYQASLKD---------------------------------------------FATRAEEKRAEAE----------------PQKKPVIKPLTEDSKKRSYNLISNDSTFTQYRSWYLAYNYGDPQTGIRSWTLLCTPDVTCGSEQVYWSLPDMMQDPVTFRSTSQISNFPVVGAELLPVHSKSFYNDQAVYSQLIRQFTSLTHVFNRFPENQILARPPAPTITTVSENVPALTDHGTLPLRNSIGGVQRVTITDARRRTCPYVYKALGIVSPRVLSSR 569
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298         -         -         -         -     | 348       | -         -    |  378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568 
                                                                                                                                                                                                                                                                                   298                                           344         356              373

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 1X9P)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: adenovirus 2 penton base, domain 2 (3)

Homologous Superfamily: adenovirus 2 penton base, domain 2 (3)

Human adenovirus 2. Organism_taxid: 10515. (2)

1x9pA02

A:131-435,A:468-520

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Penton protein; domain 1 (3)

Human adenovirus 2. Organism_taxid: 10515. (2)

1x9pA01

A:49-130,A:436-467,A:521-569

(no "Pfam Domain" information available for 1X9P)

Asymmetric Unit(hide GO term definitions)

Chain A (CAPSP_ADE02 | P03276)

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: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:0039623	T=25 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=25 symmetry. The T=25 capsid is composed of 12 pentameric and 240 hexameric capsomeres.
	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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	Cis Peptide Bonds
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Biological Unit
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	1x9p
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	CAPSP_ADE02 \| P03276	:	1x9t 2c6s 2c9f 2c9g 4v4u

1x9t	THE SAME PROTEIN COMPLEXED WITH AN AD2 N-TERMINAL FIBRE PEPTIDE

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Ligands, Modified Residues, Ions (2, 3)

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