2P7V - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI REGULATOR OF SIGMA 70, RSD, IN COMPLEX WITH SIGMA 70 DOMAIN 4

Authors :   G. A. Patikoglou, L. F. Westblade, E. A. Campbell, V. Lamour, W. J. Lane,

Date :   20 Mar 07 (Deposition) - 21 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Rsd, Sigma 70, Regulator Of Sigma 70, Sigma 70 Domain 4, Transcription, Regulation, Helix-Turn-Helix, Rsd-Sigma 70 Complex, Sigma Factor, Escherichia Coli Rsd-Sigma 70 Complex, E. Coli Rsd- Sigma 70 Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. A. Patikoglou, L. F. Westblade, E. A. Campbell, V. Lamour, W. J. Lane S. A. Darst
Crystal Structure Of The Escherichia Coli Regulator Of Sigma70, Rsd, In Complex With Sigma70 Domain 4.
J. Mol. Biol. V. 372 649 2007
PubMed-ID: 17681541 | Reference-DOI: 10.1016/J.JMB.2007.06.081

Molecule 1 - REGULATOR OF SIGMA D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RSD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - RNA POLYMERASE SIGMA FACTOR RPOD
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	DOMAIN 4
	Gene	:	RPOD, ALT
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SIGMA-70

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:1 , GLU B:605 , ARG B:608	BINDING SITE FOR RESIDUE MG B 101

(no "SS Bond" information available for 2P7V)

Asymmetric Unit

No.	Residues
1	His A:156	-	Pro A:157

(no "SAP(SNP)/Variant" information available for 2P7V)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA70_2	PS00716	Sigma-70 factors family signature 2.	RPOD_ECOLI	572-598	1	B:572-598

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA70_2	PS00716	Sigma-70 factors family signature 2.	RPOD_ECOLI	572-598	1	B:572-598

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA70_2	PS00716	Sigma-70 factors family signature 2.	RPOD_ECOLI	572-598	2	B:572-598

(no "Exon" information available for 2P7V)

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:151
 aligned with RSD_ECOLI | P0AFX4 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
            RSD_ECOLI     1 MLNQLDNLTERVRGSNKLVDRWLHVRKHLLVAYYNLVGIKPGKESYMRLNEKALDDFCQSLVDYLSAGHFSIYERILHKLEGNGQLARAAKIWPQLEANTQQIMDYYDSSLETAIDHDNYLEFQQVLSDIGEALEARFVLEDKLILLVLDAARVKHPA 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Rsd_AlgQ-2p7vA01 A:1-151                                                                                                                               ------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7v A   1 MLNQLDNLTERVRGSNKLVDRWLHVRKHLLVAYYNLVGIKPG-------NEKALDDFCQSLVDYLSAGHFSIYERILHKLEGNGQLARAAKIWPQLEANTQQIMDYYDSSLETAIDHDNYLEFQQVLSDIGEALEARFVLEDKLILLVLDAARVKHPA 158
                                    10        20        30        40 |      50        60        70        80        90       100       110       120       130       140       150        
                                                                    42      50

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with Q0P6L9_ECOLX | Q0P6L9 from UniProtKB/TrEMBL  Length:613

    Alignment length:68
                                   555       565       575       585       595       605        
         Q0P6L9_ECOLX   546 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
               SCOP domains d2p7vb_ B: Sigma70 (SigA, RpoD)                                      SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -Sigma70_r4-2p7vB01 B:547-600                          ------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2p7v B 546 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
                                   555       565       575       585       595       605

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with RPOD_ECOLI | P00579 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:68
                                   555       565       575       585       595       605        
           RPOD_ECOLI   546 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
               SCOP domains d2p7vb_ B: Sigma70 (SigA, RpoD)                                      SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -Sigma70_r4-2p7vB01 B:547-600                          ------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------SIGMA70_2  PDB: B:572-598  --------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2p7v B 546 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
                                   555       565       575       585       595       605

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: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors (41)

Family: Sigma4 domain (23)

Protein domain: Sigma70 (SigA, RpoD) (15)

Escherichia coli [TaxId: 562] (2)

d2p7vb_

(no "CATH Domain" information available for 2P7V)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Sigma70_r4 (6)

Escherichia coli (strain K12) (2)

Sigma70_r4-2p7vB01

B:547-600

Clan: no clan defined [family: Rsd_AlgQ] (1)

Family: Rsd_AlgQ (1)

Escherichia coli (strain K12) (1)

Rsd_AlgQ-2p7vA01

A:1-151

Asymmetric Unit(hide GO term definitions)

Chain A (RSD_ECOLI | P0AFX4)

molecular function
	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).
	GO:0016989	sigma factor antagonist activity	The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
biological process
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (Q0P6L9_ECOLX | Q0P6L9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016987	sigma factor activity	A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0001123	transcription initiation from bacterial-type RNA polymerase promoter	Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (RPOD_ECOLI | P00579)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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).
	GO:0016987	sigma factor activity	A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0001123	transcription initiation from bacterial-type RNA polymerase promoter	Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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	2p7v
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(no "Related Entries Specified in the PDB File" available for 2P7V)

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

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