1QRV | PD0110 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA

Authors :   F. V. Murphy Iv, R. M. Sweet, M. E. A. Churchill

Date :   15 Jun 99 (Deposition) - 18 Dec 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Protein-Dna Complex, Hmg Domain, Non-Sequence Specific Chromosomal Protein Hmg-D, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. V. Murphy 4Th. , R. M. Sweet, M. E. Churchill
The Structure Of A Chromosomal High Mobility Group Protein-Dna Complex Reveals Sequence-Neutral Mechanisms Important For Non-Sequence-Specific Dna Recognition.
Embo J. V. 18 6610 1999
PubMed-ID: 10581235 | Reference-DOI: 10.1093/EMBOJ/18.23.6610
(for further references see the PDB file header)

Compounds

*Molecule 1 - DNA (5'-D(GPCPGPAPTPAPTPCPGPC)-3')*
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - HIGH MOBILITY GROUP PROTEIN D
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET13A
	Expression System Strain	:	BL-21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-74
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	HMG-D

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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 A from PDB  Type:PROTEIN  Length:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d1qrva_ A: HMG-D                                                          SCOP domains
               CATH domains 1qrvA00 A:2-74 DNA Binding (I), subunit A                                 CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: A:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1qrv A  2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

Chain B from PDB  Type:PROTEIN  Length:71
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:71
                                    12        22        32        42        52        62        72 
            HMGD_DROME    3 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEAN 73
               SCOP domains d1qrvb_ B: HMG-D                                                        SCOP domains
               CATH domains 1qrvB00 B:3-73 DNA Binding (I), subunit A                               CATH domains
           Pfam domains (1) --HMG_box-1qrvB01 B:5-71                                             -- Pfam domains (1)
           Pfam domains (2) --HMG_box-1qrvB02 B:5-71                                             -- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HMG_BOX_2  PDB: B:5-71 UniProt: 5-71                               -- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1qrv B  3 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEAN 73
                                    12        22        32        42        52        62        72

Chain C from PDB  Type:DNA  Length:10
                                         
                  1qrv C  1 GCGATATCGC 10
                                    10

Chain D from PDB  Type:DNA  Length:10
                                         
                  1qrv D 11 GCGATATCGC 20
                                    20

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		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HMGD_DROME | Q05783)

molecular function
	GO:0003680	AT DNA binding	Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008301	DNA binding, bending	The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
biological process
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0048813	dendrite morphogenesis	The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
	GO:0007517	muscle organ development	The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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