1EA4 | PD0479 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   TRANSCRIPTIONAL REPRESSOR COPG/22BP DSDNA COMPLEX

Authors :   F. X. Gomis-Rueth, M. Costa, M. Sola, P. Acebo, R. Eritja, M. Espinosa, G. D. Solar, M. Coll

Date :   05 Nov 00 (Deposition) - 05 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : A,B,D,E,F,G,H,J,K,L,U,V,W,X,Y,Z
Biol. Unit 1: A,B,D,E,F,G,H,J,K,L,U,V,W,X,Y,Z  (2x)
Biol. Unit 2: D,E,F,G,W,X  (1x)
Biol. Unit 3: H,J,K,L,U,V  (1x)
Biol. Unit 4: A,B,Y,Z  (2x)

Keywords :   Transcriptional Repressor, Dna-Binding Protein, Plasmid, Protein-Dna Complex, Gene Regulation/Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Costa, M. Sola, G. Del, R. Eritja, A. M. Hernaindez-Arriaga, M. Espinosa, F. X. Gomis-Rueth, M. Coll
Plasmid Transcriptional Repressor Copg Oligomerises To Render Helical Superstructures Unbound And In Complexes With Oligonucleotides
J. Mol. Biol. V. 310 403 2001
PubMed-ID: 11428897 | Reference-DOI: 10.1006/JMBI.2001.4760
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REPRESSOR COPG
	Cellular Location	:	PLASMID PMV158
	Chains	:	A, B, D, E, F, G, H, J, K, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMV158
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA-BINDING PROTEIN
	Organism Scientific	:	STREPTOCOCCUS AGALACTIAE
	Organism Taxid	:	1311
	Plasmid	:	PMV158
	Synonym	:	REPA PROTEIN

*Molecule 2 - DNA (5'-D(TPAPAPCPCPGPTPGP CPAPCPTPCPAPAPTPGPCPAPAPTPC)-3')*
	Chains	:	U, W, Y
	Fragment	:	22BP SSDNA - FIRST STRAND
	Synthetic	:	YES

*Molecule 3 - DNA(5'-D(APGPAPTPTPGPCPAPTP TPGPAPGPTPGPCPAPCPGPGPTPT)-3')*
	Chains	:	V, X, Z
	Fragment	:	22BP SSDNA - SECOND STRAND
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	B	D	E	F	G	H	J	K	L	U	V	W	X	Y	Z
Biological Unit 1 (2x)	:	A	B	D	E	F	G	H	J	K	L	U	V	W	X	Y	Z
Biological Unit 2 (1x)	:			D	E	F	G							W	X
Biological Unit 3 (1x)	:							H	J	K	L	U	V
Biological Unit 4 (2x)	:	A	B													Y	Z

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1EA4)

(no "Site" information available for 1EA4)

(no "SS Bond" information available for 1EA4)

(no "Cis Peptide Bond" information available for 1EA4)

(no "SAP(SNP)/Variant" information available for 1EA4)

(no "PROSITE Motif" information available for 1EA4)

(no "Exon" information available for 1EA4)

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:42
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:42
                                    11        21        31        41  
           COPG_STRAG     2 KKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ  43
               SCOP domains d1ea4a_ A: Transcriptional repressor CopG  SCOP domains
               CATH domains 1ea4A00 A:2-43 Met repressor-like          CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 1ea4 A   2 KKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ  43
                                    11        21        31        41

Chain B from PDB  Type:PROTEIN  Length:41
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:41
                                    10        20        30        40 
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKK  41
               SCOP domains d1ea4b_ B: Transcriptional repressor CopG SCOP domains
               CATH domains 1ea4B00 B:1-41 Met repressor-like         CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 1ea4 B   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKK  41
                                    10        20        30        40

Chain D from PDB  Type:PROTEIN  Length:43
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:43
                                    10        20        30        40   
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ  43
               SCOP domains d1ea4d_ D: Transcriptional repressor CopG   SCOP domains
               CATH domains 1ea4D00 D:1-43 Met repressor-like           CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 1ea4 D   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ  43
                                    10        20        30        40

Chain E from PDB  Type:PROTEIN  Length:44
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:44
                                    10        20        30        40    
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQE  44
               SCOP domains d1ea4e_ E: Transcriptional repressor CopG    SCOP domains
               CATH domains 1ea4E00 E:1-44 Met repressor-like            CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 1ea4 E   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQE  44
                                    10        20        30        40

Chain F from PDB  Type:PROTEIN  Length:45
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:45
                                    10        20        30        40     
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK  45
               SCOP domains d1ea4f_ F: Transcriptional repressor CopG     SCOP domains
               CATH domains 1ea4F00 F:1-45 Met repressor-like             CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 1ea4 F   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK  45
                                    10        20        30        40

Chain G from PDB  Type:PROTEIN  Length:42
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:42
                                    10        20        30        40  
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKG  42
               SCOP domains d1ea4g_ G: Transcriptional repressor CopG  SCOP domains
               CATH domains 1ea4G00 G:1-42 Met repressor-like          CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 1ea4 G   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKG  42
                                    10        20        30        40

Chain H from PDB  Type:PROTEIN  Length:44
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:44
                                    11        21        31        41    
           COPG_STRAG     2 KKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK  45
               SCOP domains d1ea4h_ H: Transcriptional repressor CopG    SCOP domains
               CATH domains 1ea4H00 H:2-45 Met repressor-like            CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 1ea4 H   2 KKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK  45
                                    11        21        31        41

Chain J from PDB  Type:PROTEIN  Length:44
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:44
                                    10        20        30        40    
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQE  44
               SCOP domains d1ea4j_ J: Transcriptional repressor CopG    SCOP domains
               CATH domains 1ea4J00 J:1-44 Met repressor-like            CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 1ea4 J   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQE  44
                                    10        20        30        40

Chain K from PDB  Type:PROTEIN  Length:43
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:43
                                    10        20        30        40   
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ  43
               SCOP domains d1ea4k_ K: Transcriptional repressor CopG   SCOP domains
               CATH domains 1ea4K00 K:1-43 Met repressor-like           CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 1ea4 K   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ  43
                                    10        20        30        40

Chain L from PDB  Type:PROTEIN  Length:44
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:44
                                    10        20        30        40    
           COPG_STRAG     1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQE  44
               SCOP domains d1ea4l_ L: Transcriptional repressor CopG    SCOP domains
               CATH domains 1ea4L00 L:1-44 Met repressor-like            CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 1ea4 L   1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQE  44
                                    10        20        30        40

Chain U from PDB  Type:DNA  Length:20
                                                    
                 1ea4 U 202 AACCGTGCACTCAATGCAAT 221
                                   211       221

Chain V from PDB  Type:DNA  Length:21
                                                     
                 1ea4 V 201 AGATTGCATTGAGTGCACGGT 221
                                   210       220

Chain W from PDB  Type:DNA  Length:22
                                                      
                 1ea4 W 201 TAACCGTGCACTCAATGCAATC 222
                                   210       220

Chain X from PDB  Type:DNA  Length:22
                                                      
                 1ea4 X 201 AGATTGCATTGAGTGCACGGTT 222
                                   210       220

Chain Y from PDB  Type:DNA  Length:21
                                                     
                 1ea4 Y 202 AACCGTGCACTCAATGCAATC 222
                                   211       221

Chain Z from PDB  Type:DNA  Length:21
                                                     
                 1ea4 Z 201 AGATTGCATTGAGTGCACGGT 221
                                   210       220

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: CopG-like (13)

Protein domain: Transcriptional repressor CopG (3)

Streptococcus agalactiae [TaxId: 1311] (3)

1a	d1ea4a_	A:
1b	d1ea4g_	G:
1c	d1ea4h_	H:
1d	d1ea4j_	J:
1e	d1ea4k_	K:
1f	d1ea4l_	L:
1g	d1ea4b_	B:
1h	d1ea4d_	D:
1i	d1ea4e_	E:
1j	d1ea4f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant (30)

Homologous Superfamily: Met repressor-like (30)

Streptococcus agalactiae. Organism_taxid: 1311. (1)

1a	1ea4F00	F:1-45
1b	1ea4E00	E:1-44
1c	1ea4H00	H:2-45
1d	1ea4J00	J:1-44
1e	1ea4L00	L:1-44
1f	1ea4D00	D:1-43
1g	1ea4K00	K:1-43
1h	1ea4A00	A:2-43
1i	1ea4G00	G:1-42
1j	1ea4B00	B:1-41

(no "Pfam Domain" information available for 1EA4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,E,F,G,H,J,K,L (COPG_STRAG | P13920)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0006276	plasmid maintenance	The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates 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.

Asymmetric Unit
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(no "Cis Peptide Bonds" information available for 1ea4)

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	1ea4
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	COPG_STRAG \| P13920
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	COPG_STRAG \| P13920	:	1b01 2cpg

1b01	TRANSCRIPTIONAL REPRESSOR COPG/DEOXYRIBONUCLEIC ACID COMPLEX
2cpg	TRANSCRIPTIONAL REPRESSOR COPG

Description

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