3NM9 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   HMGD(M13A)-DNA COMPLEX

Authors :   M. E. A. Churchill, J. Klass, D. L. Zoetewey

Date :   22 Jun 10 (Deposition) - 22 Sep 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P

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

Reference :   M. E. Churchill, J. Klass, D. L. Zoetewey
Structural Analysis Of Hmgd-Dna Complexes Reveals Influence Of Intercalation On Sequence Selectivity And Dna Bending.
J. Mol. Biol. V. 403 88 2010
PubMed-ID: 20800069 | Reference-DOI: 10.1016/J.JMB.2010.08.031

Molecule 1 - HIGH MOBILITY GROUP PROTEIN D
	Chains	:	A, D, G, J, M, P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-D74-M13A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET13A
	Gene	:	CG17950, HMGD
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	HMG-D

*Molecule 2 - DNA 5'-D(GGPCPGPAPTPAPTPCPGPC)-3'**
	Chains	:	B, C, E, F, H, I, K, L, N, O
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3NM9)

(no "Site" information available for 3NM9)

(no "SS Bond" information available for 3NM9)

(no "Cis Peptide Bond" information available for 3NM9)

(no "SAP(SNP)/Variant" information available for 3NM9)

Asymmetric/Biological Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMG_BOX_2	PS50118	HMG boxes A and B DNA-binding domains profile.	HMGD_DROME	5-71	6	A:5-71 D:5-71 G:5-71 J:5-71 M:5-71 P:5-71

(no "Exon" information available for 3NM9)

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 d3nm9a_ A: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: A:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 A  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

Chain B from PDB  Type:DNA  Length:10
                                         
                  3nm9 B  2 GCGATATCGC 11
                                    11

Chain C from PDB  Type:DNA  Length:10
                                         
                  3nm9 C  2 GCGATATCGC 11
                                    11

Chain D 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 d3nm9d_ D: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: D:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 D  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

Chain E from PDB  Type:DNA  Length:10
                                         
                  3nm9 E  2 GCGATATCGC 11
                                    11

Chain F from PDB  Type:DNA  Length:10
                                         
                  3nm9 F  2 GCGATATCGC 11
                                    11

Chain G 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 d3nm9g_ G: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: G:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 G  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

Chain H from PDB  Type:DNA  Length:10
                                         
                  3nm9 H  2 GCGATATCGC 11
                                    11

Chain I from PDB  Type:DNA  Length:10
                                         
                  3nm9 I  2 GCGATATCGC 11
                                    11

Chain J 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 d3nm9j_ J: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: J:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 J  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

Chain K from PDB  Type:DNA  Length:10
                                         
                  3nm9 K  2 GCGATATCGC 11
                                    11

Chain L from PDB  Type:DNA  Length:11
                                          
                  3nm9 L  1 GGCGATATCGC 11
                                    10

Chain M 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 d3nm9m_ M: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: M:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 M  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

Chain N from PDB  Type:DNA  Length:10
                                         
                  3nm9 N  2 GCGATATCGC 11
                                    11

Chain O from PDB  Type:DNA  Length:10
                                         
                  3nm9 O  2 GCGATATCGC 11
                                    11

Chain P 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 d3nm9p_ P: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---HMG_box-3nm9P01 P:5-71                                             --- Pfam domains (1)
           Pfam domains (2) ---HMG_box-3nm9P02 P:5-71                                             --- Pfam domains (2)
           Pfam domains (3) ---HMG_box-3nm9P03 P:5-71                                             --- Pfam domains (3)
           Pfam domains (4) ---HMG_box-3nm9P04 P:5-71                                             --- Pfam domains (4)
           Pfam domains (5) ---HMG_box-3nm9P05 P:5-71                                             --- Pfam domains (5)
           Pfam domains (6) ---HMG_box-3nm9P06 P:5-71                                             --- Pfam domains (6)
         Sec.struct. author ........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: P:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 P  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: HMG-box (49)

Superfamily: HMG-box (49)

Family: HMG-box (43)

Protein domain: automated matches (9)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (2)

1a	d3nm9a_	A:
1b	d3nm9d_	D:
1c	d3nm9g_	G:
1d	d3nm9j_	J:
1e	d3nm9m_	M:
1f	d3nm9p_	P:

(no "CATH Domain" information available for 3NM9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HMG-box (15)

Family: HMG_box (14)

Drosophila melanogaster (Fruit fly) (3)

1a	HMG_box-3nm9P01	P:5-71
1b	HMG_box-3nm9P02	P:5-71
1c	HMG_box-3nm9P03	P:5-71
1d	HMG_box-3nm9P04	P:5-71
1e	HMG_box-3nm9P05	P:5-71
1f	HMG_box-3nm9P06	P:5-71

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,D,G,J,M,P (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.

Asymmetric/Biological Unit
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(no "Sites" information available for 3nm9)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nm9)

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	3nm9
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	HMGD_DROME \| Q05783
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	HMGD_DROME \| Q05783
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UniProtKB/Swiss-Prot
	HMGD_DROME \| Q05783	:	1e7j 1hma 1qrv

1qrv	CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

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SCOP Domains (1, 6)

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Pfam Domains (1, 6)

Gene Ontology (9, 9)

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