2O97 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI HU HETERODIMER

Authors :   F. Guo, S. Adhya

Date :   13 Dec 06 (Deposition) - 06 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A,B  (1x)

Keywords :   Dna-Binding, Heterodimer, Dna Structure, Dna Supercoiling, E. Coli, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Guo, S. Adhya
Spiral Structure Of Escherichia Coli Hu{Alpha}Beta Provides Foundation For Dna Supercoiling.
Proc. Natl. Acad. Sci. Usa V. 104 4309 2007
PubMed-ID: 17360520 | Reference-DOI: 10.1073/PNAS.0611686104

Molecule 1 - DNA-BINDING PROTEIN HU-ALPHA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRLM118
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HUPA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	NS2, HU-2

Molecule 2 - DNA-BINDING PROTEIN HU-BETA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRLM118
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HUPB, HOPD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	NS1, HU-1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	NI	1	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:110	BINDING SITE FOR RESIDUE CL B 102
2	AC2	SOFTWARE	MET A:1 , ASP B:40 , HOH B:108 , HOH B:109 , HOH B:110	BINDING SITE FOR RESIDUE NI B 101

(no "SS Bond" information available for 2O97)

(no "Cis Peptide Bond" information available for 2O97)

(no "SAP(SNP)/Variant" information available for 2O97)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBHA_ECOLI	46-65	1	A:46-54
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBHB_ECOLI	46-65	1	B:46-55

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBHA_ECOLI	46-65	4	A:46-54
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBHB_ECOLI	46-65	4	B:46-55

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBHA_ECOLI	46-65	1	A:46-54
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBHB_ECOLI	46-65	1	B:46-55

(no "Exon" information available for 2O97)

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:70
 aligned with DBHA_ECOLI | P0ACF0 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
            DBHA_ECOLI    1 MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK 90
               SCOP domains d2o97a_ A: HU protein                                                                      SCOP domains
               CATH domains 2o97A00 A:1-90 HU Protein, subunit A                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeee.--------------------.eeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------HISTONE_LIKE        ------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  2o97 A  1 MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNH--------------------NVPAFVSGKALKDAVK 90
                                    10        20        30        40        50   |     -         -    |   80        90
                                                                                54                   75

Chain B from PDB  Type:PROTEIN  Length:71
 aligned with DBHB_ECOLI | P0ACF4 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
            DBHB_ECOLI    1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFRAGKALKDAVN 90
               SCOP domains d2o97b1 B:1-90  HU protein                                                                 SCOP domains
               CATH domains 2o97B00 B:1-90  HU Protein, subunit A                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..-hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeee..------------------..eeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------------HISTONE_LIKE        ------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  2o97 B  1 MNKSQLIDKIAAGAD-SKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKER------------------AKVPSFRAGKALKDAVN 90
                                    10    | | 20        30        40        50    |    -         -   |    80        90
                                         15 |                                    55                 74                
                                           17

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: IHF-like DNA-binding proteins (28)

Superfamily: IHF-like DNA-binding proteins (28)

Family: Prokaryotic DNA-bending protein (23)

Protein domain: HU protein (10)

Escherichia coli [TaxId: 562] (2)

d2o97a_

Escherichia coli, beta-isoform [TaxId: 562] (1)

d2o97b1

B:1-90

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: HU Protein; Chain A (18)

Homologous Superfamily: HU Protein, subunit A (18)

Escherichia coli. Organism_taxid: 562. (2)

1a	2o97A00	A:1-90
1b	2o97B00	B:1-90

(no "Pfam Domain" information available for 2O97)

Asymmetric Unit(hide GO term definitions)

Chain A (DBHA_ECOLI | P0ACF0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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).
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:1990178	HU-DNA complex	A protein-DNA complex that consists of HU heterodimers (an alpha and a beta chain) assembled into octamers along DNA. HU binds to double-stranded DNA in a structure- and sequence-specific manner and bends the DNA into a nucleosome-like structure.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B (DBHB_ECOLI | P0ACF4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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).
biological process
	GO:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	2o97
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(no "Related Entries Specified in the PDB File" available for 2O97)

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