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Title :   2.1 RESOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF THE HUMAN ADENOVIRUS 5 SSDNA BINDING PROTEIN

Authors :   J. Hendle, P. N. Kanellopoulos, P. A. Tucker

Date :   19 Feb 09 (Deposition) - 31 Mar 10 (Release) - 31 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : X

Keywords :   Dna-Binding Protein, Ssdna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Hendle, P. N. Kanellopoulos, P. A. Tucker
High Resolution Structures Of The Adenovirus Single-Stranded Dna Binding Protein And The N512P Hinge-Region Mutant
To Be Published
PubMed: search

Molecule 1 - E2A DNA-BINDING PROTEIN
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	C-TERMINAL DNA BINDING DOMAIN, RESIDUES 174-529
	Organism Scientific	:	HUMAN ADENOVIRUS 5
	Organism Taxid	:	28285
	Synonym	:	ADENOVIRUS 5 SSDNA BINDING PROTEIN

		1
Asymmetric/Biological Unit	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS X:284 , HIS X:286 , CYS X:339 , CYS X:355	BINDING SITE FOR RESIDUE ZN X 601
2	AC2	SOFTWARE	CYS X:396 , CYS X:398 , CYS X:450 , CYS X:467	BINDING SITE FOR RESIDUE ZN X 602

(no "SS Bond" information available for 2WB0)

(no "Cis Peptide Bond" information available for 2WB0)

(no "SAP(SNP)/Variant" information available for 2WB0)

(no "PROSITE Motif" information available for 2WB0)

(no "Exon" information available for 2WB0)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain X from PDB  Type:PROTEIN  Length:314
 aligned with DNB2_ADE05 | P03265 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:353
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526   
           DNB2_ADE05   177 IVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSKKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIEMDVTSENGQRALKEQSSKAKIVKNRWGRNVVQISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVYRNSRAQGGGPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRNVSLPVAHSDARQNPFDF 529
               SCOP domains d2wb0x1 X:177-265 Domain of early E2A DNA-binding protein, ADDBP                         d2wb0x2 X:266-385 First Zn-domain                                of early E2A DNA-binding protein, ADDBP                d2wb0x3 X:386-529 Second Zn-domain of early E2A DNA-binding protein, A        DDBP                                                               SCOP domains
               CATH domains 2wb0X01 X:177-266,X:474-500 Adenovirus Single-stranded Dna-binding Protein, domain 1      2wb0X02 X:267-473 Adenovirus Sin                               gle-stranded Dna-binding Protein, domain 2                                                                                                      2wb0X01 X:177-266,X:474-500----------------------------- CATH domains
           Pfam domains (1) Viral_DNA_bi-2wb0X03 X:177-264                                                          ----------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wb0X01 X:394-519                                                                                             ---------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wb0X02 X:394-519                                                                                             ---------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..........eeeee..................eeeeeee.-------------------------------.eeeeeeee.hhhh..............ee.hhhhhhhhhhhhhhhhhhhh........eeeee.....................eeeee.......hhhhh.hhhhhhhhhh.eeeeee......--------......eeehhhhhhhhhhhhhhhhh...............hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wb0 X 177 IVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSNKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIE-------------------------------QISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVY--------GPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRNVSLPVAHSDARQNPFDF 529
                                   186       196       206       216       226       236       246       256       266       276       286       296 |       -         -         -   |   336       346       356       366       376       386       396       406       416       426       436       446        |-       466       476       486       496       506       516       526   
                                                                                                                                                   298                             330                                                                                                                          455      464

Chain X from PDB  Type:PROTEIN  Length:314
 aligned with Q6VGU4_ADE05 | Q6VGU4 from UniProtKB/TrEMBL  Length:529

    Alignment length:353
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526   
         Q6VGU4_ADE05   177 IVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSNKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIEMDVTSENGQRALKEQSSKAKIVKNRWGRNVVQISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVYRNSRAQGGGPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRNVSLPVAHSDARQNPFDF 529
               SCOP domains d2wb0x1 X:177-265 Domain of early E2A DNA-binding protein, ADDBP                         d2wb0x2 X:266-385 First Zn-domain                                of early E2A DNA-binding protein, ADDBP                d2wb0x3 X:386-529 Second Zn-domain of early E2A DNA-binding protein, A        DDBP                                                               SCOP domains
               CATH domains 2wb0X01 X:177-266,X:474-500 Adenovirus Single-stranded Dna-binding Protein, domain 1      2wb0X02 X:267-473 Adenovirus Sin                               gle-stranded Dna-binding Protein, domain 2                                                                                                      2wb0X01 X:177-266,X:474-500----------------------------- CATH domains
           Pfam domains (1) Viral_DNA_bi-2wb0X03 X:177-264                                                          ----------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wb0X01 X:394-519                                                                                             ---------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------                               ----------------------------------------------------------------Viral_DNA_Zn_bi-2wb0X02 X:394-519                                                                                             ---------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..........eeeee..................eeeeeee.-------------------------------.eeeeeeee.hhhh..............ee.hhhhhhhhhhhhhhhhhhhh........eeeee.....................eeeee.......hhhhh.hhhhhhhhhh.eeeeee......--------......eeehhhhhhhhhhhhhhhhh...............hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wb0 X 177 IVSAWEKGMEAARALMDKYHVDNDLKANFKLLPDQVEALAAVCKTWLNEEHRGLQLTFTSNKTFVTMMGRFLQAYLQSFAEVTYKHHEPTGCALWLHRCAEIEGELKCLHGSIMINKEHVIE-------------------------------QISNTDARCCVHDAACPANQFSGKSCGMFFSEGAKAQVAFKQIKAFMQALYPNAQTGHGHLLMPLRCECNSKPGHAPFLGRQLPKLTPFALSNAEDLDADLISDKSVLASVHHPALIVFQCCNPVY--------GPNCDFKISAPDLLNALVMVRSLWSENFTELPRMVVPEFKWSTKHQYRNVSLPVAHSDARQNPFDF 529
                                   186       196       206       216       226       236       246       256       266       276       286       296 |       -         -         -   |   336       346       356       366       376       386       396       406       416       426       436       446        |-       466       476       486       496       506       516       526   
                                                                                                                                                   298                             330                                                                                                                          455      464

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 '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (Q6VGU4_ADE05 | Q6VGU4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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.

Chain X (DNB2_ADE05 | P03265)

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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0045740	positive regulation of DNA replication	Any process that activates or increases the frequency, rate or extent of DNA replication.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.
	GO:0039687	viral DNA strand displacement replication	A viral DNA replication process where only one strand is replicated at once, and which releases a single stranded DNA (ssDNA).
	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: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.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	DNB2_ADE05 \| P03265	:	1adu 1adv 1anv 2waz
	Q6VGU4_ADE05 \| Q6VGU4	:	2waz

1anv	ADENOVIRUS 5 DBP/URANYL FLUORIDE SOAK
2waz	N512P MUTANT OF THE DNA BINDING DOMAIN OF THE ADENOVIRUS 5 SSDNA BINDING PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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SCOP Domains (3, 3)

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