2Q1Z - JenaLib

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Title :   CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES SIGE IN COMPLEX WITH THE ANTI-SIGMA CHRR

Authors :   E. A. Campbell, S. A. Darst

Date :   25 May 07 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Ecf Sigma Factor, Anti-Sigma Factor, Cupin Fold, Zinc Binding Transcription Factor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. A. Campbell, R. Greenwell, J. R. Anthony, S. Wang, L. Lim, K. Das, H. J. Sofia, T. J. Donohue, S. A. Darst
A Conserved Structural Module Regulates Transcriptional Responses To Diverse Stress Signals In Bacteria.
Mol. Cell V. 27 793 2007
PubMed-ID: 17803943 | Reference-DOI: 10.1016/J.MOLCEL.2007.07.009

Molecule 1 - RPOE, ECF SIGE
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A DERIVITIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RPOE
	Organism Scientific	:	RHODOBACTER SPHAEROIDES
	Organism Taxid	:	272943
	Strain	:	2.4.1

Molecule 2 - ANTI-SIGMA FACTOR CHRR, TRANSCRIPTIONAL ACTIVATOR CHRR
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A DERIVITIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CHRR
	Organism Scientific	:	RHODOBACTER SPHAEROIDES
	Organism Taxid	:	272943
	Strain	:	2.4.1

		1	2	3	4
Asymmetric Unit (2x)	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:6 , HIS B:31 , CYS B:35 , CYS B:38	BINDING SITE FOR RESIDUE ZN B 196
2	AC2	SOFTWARE	HIS B:141 , HIS B:143 , GLU B:147 , HIS B:177	BINDING SITE FOR RESIDUE ZN B 197
3	AC3	SOFTWARE	HIS D:6 , HIS D:31 , CYS D:35 , CYS D:38	BINDING SITE FOR RESIDUE ZN D 196
4	AC4	SOFTWARE	HIS D:141 , HIS D:143 , GLU D:147 , HIS D:177	BINDING SITE FOR RESIDUE ZN D 197

(no "SS Bond" information available for 2Q1Z)

Asymmetric Unit

No.	Model	Residues
1	1, 2	Leu B:110	-	Gly B:111
2	1	Leu C:162	-	Gly C:163
3	2	Gly C:159	-	Leu C:160

(no "SAP(SNP)/Variant" information available for 2Q1Z)

(no "PROSITE Motif" information available for 2Q1Z)

(no "Exon" information available for 2Q1Z)

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:176
 aligned with RPOE_RHOS4 | Q3IYV6 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      
           RPOE_RHOS4     5 SDRTDWVALMRAIRDHRDEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRASVATWIFTIARNRRIDGLRKDRQPEPEDLFWGPDSEPDQADVYEMQQENARLGRAIARLPEAQRALIERAFFGDLTHRELAAETGLPLGTIKSRIRLALDRLRQHM 180
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1z A   5 SDRTDWVALMRAIRDHRDEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRASVATWIFTIARNRRIDGLRKDRQPEPEDLFWGPDSEPDQADVYEMQQENARLGRAIARLPEAQRALIERAFFGDLTHRELAAETGLPLGTIKSRIRLALDRLRQHM 180
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with CHRR_RHOS4 | P40685 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
           CHRR_RHOS4     2 TIRHHVSDALLTAYAAGTLSEAFSLVVATHLSLCDECRARAGALDAVGGSLMEETAPVALSEGSLASVMAQLDRQIQRPAPARRADPRAPAPLADYVGRRLEDVRWRTLGGGVRQAILPTGGEAIARLLWIPGGQAVPDHGHRGLELTLVLQGAFRDETDRFGAGDIEIADQELEHTPVAERGLDCICLAATD 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.....--------.......hhhhhhh........ee.....eeeee......eeeeeee..............eeeeeee.eee....eee...eeee........ee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1z B   2 TIRHHVSDALLTAYAAGTLSEAFSLVVATHLSLCDECRARAGALDAVGGSLMEETAPVALSEGSLASVMAQLDRQI--------ADPRAPAPLADYVGRRLEDVRWRTLGGGVRQAILPTGGEAIARLLWIPGGQAVPDHGHRGLELTLVLQGAFRDETDRFGAGDIEIADQELEHTPVAERGLDCICLAATD 194
                                    11        21        31        41        51        61        71     |   -    |   91       101       111       121       131       141       151       161       171       181       191   
                                                                                                      77       86

Chain C from PDB  Type:PROTEIN  Length:164
 aligned with RPOE_RHOS4 | Q3IYV6 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
           RPOE_RHOS4     5 SDRTDWVALMRAIRDHRDEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRASVATWIFTIARNRRIDGLRKDRQPEPEDLFWGPDSEPDQADVYEMQQENARLGRAIARLPEAQRALIERAFFGDLTHRELAAETGLPLGTIKSRIRLALDR 175
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhh-------hhhhhhhhh.................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1z C   5 SDRTDWVALMRAIRDHRDEAAFAELFQHFAPKVKGFLMKSGSVASQAEECAQDVMATVWQKAHLFDPSRASVATWIFTIARNRRIDGLRKDRQPEPEDLFWGPDSEPDQADVYEMQQENARLGRAIA-------ALIERAFFGDLTHRELAAETGLPLGTIKSRIRLALDR 175
                                    14        24        34        44        54        64        74        84        94       104       114       124      |  -    |  144       154       164       174 
                                                                                                                                                        131     139

Chain D from PDB  Type:PROTEIN  Length:181
 aligned with CHRR_RHOS4 | P40685 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
           CHRR_RHOS4     2 TIRHHVSDALLTAYAAGTLSEAFSLVVATHLSLCDECRARAGALDAVGGSLMEETAPVALSEGSLASVMAQLDRQIQRPAPARRADPRAPAPLADYVGRRLEDVRWRTLGGGVRQAILPTGGEAIARLLWIPGGQAVPDHGHRGLELTLVLQGAFRDETDRFGAGDIEIADQELEHTPVAERGLDCICLAATD 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---zf-HC2-2q1zD03 D:5-40               -----------------------------------------------------------------Cupin_7-2q1zD01 D:106-194                                                                 Pfam domains (1)
           Pfam domains (2) ---zf-HC2-2q1zD04 D:5-40               -----------------------------------------------------------------Cupin_7-2q1zD02 D:106-194                                                                 Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh...------------......hhhhhhh.hhhhh.........eeeee......eeeeeee..............eeeeeee.eee....eee...eeee........ee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1z D   2 TIRHHVSDALLTAYAAGTLSEAFSLVVATHLSLCDECRARAGALDAVGGSLMEETAPVALSEGSLASVMAQLD------------DPRAPAPLADYVGRRLEDVRWRTLGGGVRQAILPTGGEAIARLLWIPGGQAVPDHGHRGLELTLVLQGAFRDETDRFGAGDIEIADQELEHTPVAERGLDCICLAATD 194
                                    11        21        31        41        51        61        71  |      -     |  91       101       111       121       131       141       151       161       171       181       191   
                                                                                                   74           87

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 '\|'

(no "SCOP Domain" information available for 2Q1Z)

(no "CATH Domain" information available for 2Q1Z)

Asymmetric Unit(hide GO term definitions)

Chain A,C (RPOE_RHOS4 | Q3IYV6)

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: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.

Chain B,D (CHRR_RHOS4 | P40685)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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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	Cis Peptide Bonds
		Gly C:159 - Leu C:160	[ RasMol ]
		Leu B:110 - Gly B:111	[ RasMol ]
		Leu C:162 - Gly C:163	[ RasMol ]

Biological Units
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	2q1z
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	RPOE_RHOS4 \| Q3IYV6
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	CHRR_RHOS4 \| P40685	:	2z2s
	RPOE_RHOS4 \| Q3IYV6	:	2z2s

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Pfam Domains (2, 4)

Gene Ontology (7, 10)

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