1X9T - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PENTON BASE IN COMPLEX WITH AN AD2 N-TERMINAL FIBRE PEPTIDE

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 :   3.50

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

Keywords :   Jellyroll Domain, Insertion Domain, Anti-Parallel Beta Sheets, Virus Like Particle/Peptide Complex (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

Molecule 2 - N-TERMINL PEPTIDE OF FIBER PROTEIN
	Chains	:	B
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (60x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 120)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:263 , GLY A:270 , ARG A:272 , TRP A:422 , C15 A:2000	BINDING SITE FOR RESIDUE C15 A 1014
2	AC2	SOFTWARE	ARG A:146 , TRP A:165 , ARG A:272 , C15 A:1014	BINDING SITE FOR RESIDUE C15 A 2000

(no "SS Bond" information available for 1X9T)

(no "Cis Peptide Bond" information available for 1X9T)

(no "SAP(SNP)/Variant" information available for 1X9T)

(no "PROSITE Motif" information available for 1X9T)

(no "Exon" information available for 1X9T)

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:440
 aligned with CAPSP_ADE02 | P03276 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:518
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561        
          CAPSP_ADE02    52 RNSIRYSELAPLFDTTRVYLVDNKSTDVASLNYQNDHSNFLTTVIQNNDYSPGEASTQTINLDDRSHWGGDLKTILHTNMPNVNEFMFTNKFKARVMVSRSLTKDKQVELKYEWVEFTLPEGNYSETMTIDLMNNAIVEHYLKVGRQNGVLESDIGVKFDTRNFRLGFDPVTGLVMPGVYTNEAFHPDIILLPGCGVDFTHSRLSNLLGIRKRQPFQEGFRITYDDLEGGNIPALLDVDAYQASLKDDTEQGGDGAGGGNNSGSGAEENSNAAAAAMQPVEDMNDHAIRGDTFATRAEEKRAEAEAAAEAAAPAAQPEVEKPQKKPVIKPLTEDSKKRSYNLISNDSTFTQYRSWYLAYNYGDPQTGIRSWTLLCTPDVTCGSEQVYWSLPDMMQDPVTFRSTSQISNFPVVGAELLPVHSKSFYNDQAVYSQLIRQFTSLTHVFNRFPENQILARPPAPTITTVSENVPALTDHGTLPLRNSIGGVQRVTITDARRRTCPYVYKALGIVSPRVLSSR 569
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x9tA01 A:52-130,A:436-467,A:521-569 Penton protein; domain 1                  1x9tA02 A:131-435,A:468-520 adenovirus 2 penton base, domain 2                                                                                                                                                                                                                                                   1x9tA01 Penton protein; domain 11x9tA02 A:131-435,A:468-520                          1x9tA01 A:52-130,A:436-467,A:521-569              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...........eeee..hhhhhhh........eeeee.........hhhhhheeee...eeeeeeeeeeeee............eeeeeeeeeeeee...eeeeeeeeeeee......hhhhhhhhhhhhhhhhhh..hhhhh........eeeee...........ee........eeeeeeee....eee....hhhhhhheee........eee.......eeeee.hhhhhhhh.------------------------------------------------------------------------------..........hhhhh..........eeeeeehhhhhhhh.........eee..........eeee........................eeee..eeeee.......hhhhhhhhhh.......................eeeee..eeeeeeeee...eee.eeeee.ee........eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9t A  52 RNSIRYSELAPLFDTTRVYLVDNKSTDVASLNYQNDHSNFLTTVIQNNDYSPGEASTQTINLDDRSHWGGDLKTILHTNMPNVNEFMFTNKFKARVMVSRSLTKDKQVELKYEWVEFTLPEGNYSETMTIDLMNNAIVEHYLKVGRQNGVLESDIGVKFDTRNFRLGFDPVTGLVMPGVYTNEAFHPDIILLPGCGVDFTHSRLSNLLGIRKRQPFQEGFRITYDDLEGGNIPALLDVDAYQASL------------------------------------------------------------------------------KKPVIKPLTEDSKKRSYNLISNDSTFTQYRSWYLAYNYGDPQTGIRSWTLLCTPDVTCGSEQVYWSLPDMMQDPVTFRSTSQISNFPVVGAELLPVHSKSFYNDQAVYSQLIRQFTSLTHVFNRFPENQILARPPAPTITTVSENVPALTDHGTLPLRNSIGGVQRVTITDARRRTCPYVYKALGIVSPRVLSSR 569
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291    |    -         -         -         -         -         -         -         -   |   381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561        
                                                                                                                                                                                                                                                                              296                                                                            375

Chain B from PDB  Type:PROTEIN  Length:10
 aligned with SPIKE_ADE02 | P03275 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:10
                                    19
          SPIKE_ADE02    10 TFNPVYPYDT  19
               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
                 1x9t B  10 TFNPVYPYDT  19
                                    19

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 1X9T)

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)

1x9tA02

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)

1x9tA01

A:52-130,A:436-467,A:521-569

(no "Pfam Domain" information available for 1X9T)

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.

Chain B (SPIKE_ADE02 | P03275)

biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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: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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	CAPSP_ADE02 \| P03276	:	1x9p 2c6s 2c9f 2c9g 4v4u
	SPIKE_ADE02 \| P03275	:	1qhv 1qiu 1v1h 1v1i 2c9f 4ar2 4v4u

1x9p	CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PENTON BASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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