3T0Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE PHYR ANTI-ANTI-SIGMA DOMAIN BOUND TO THE ANTI-SIGMA FACTOR, NEPR

Authors :   J. Herrou, S. Crosson

Date :   20 Jul 11 (Deposition) - 02 May 12 (Release) - 27 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Sigma Factor, Anti-Sigma Factor, Receiver Domain, Gene Regulation, Signal Transduction, Transcription Regulator-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Herrou, G. Rotskoff, Y. Luo, B. Roux, S. Crosson
Structural Basis Of A Protein Partner Switch That Regulates The General Stress Response Of Alpha-Proteobacteria
Proc. Natl. Acad. Sci. Usa V. 109 E1415 2012
PubMed-ID: 22550172 | Reference-DOI: 10.1073/PNAS.1116887109

Molecule 1 - RESPONSE REGULATOR
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-DUET
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-141
	Gene	:	CC_3477, PHYR
	Organism Scientific	:	CAULOBACTER VIBRIOIDES
	Organism Taxid	:	155892
	Strain	:	NA1000

Molecule 2 - NEPR
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-DUET
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CC_3476, NEPR
	Organism Scientific	:	CAULOBACTER VIBRIOIDES
	Organism Taxid	:	155892
	Strain	:	NA1000

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3T0Y)

(no "SS Bond" information available for 3T0Y)

Asymmetric/Biological Unit

No.	Residues
1	Ala C:82	-	Gly C:83

(no "SAP(SNP)/Variant" information available for 3T0Y)

(no "PROSITE Motif" information available for 3T0Y)

(no "Exon" information available for 3T0Y)

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:126
 aligned with A0A0H3CBZ6_C | A0A0H3CBZ6 from UniProtKB/TrEMBL  Length:266

    Alignment length:139
                             1                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129         
         A0A0H3CBZ6_C     - -MSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSSGAQLEVGHDQGLHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAE 138
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..h-------------hhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0y A  14 PmSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSS-------------AGDDAAQRLmRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAE 139
                             |      23        33        43        53        63        73       | -         - |      90|      100       110       120       130         
                             |                                                                81            82       91-MSE                                            
                            15-MSE

Chain A from PDB  Type:PROTEIN  Length:126
 aligned with Q9A2S9_CAUCR | Q9A2S9 from UniProtKB/TrEMBL  Length:266

    Alignment length:139
                             1                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129         
         Q9A2S9_CAUCR     - -MSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSSGAQLEVGHDQGLHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAE 138
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..h-------------hhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0y A  14 PmSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSS-------------AGDDAAQRLmRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAE 139
                             |      23        33        43        53        63        73       | -         - |      90|      100       110       120       130         
                            15-MSE                                                            81            82       91-MSE

Chain B from PDB  Type:PROTEIN  Length:33
 aligned with A0A0H3CFC9_C | A0A0H3CFC9 from UniProtKB/TrEMBL  Length:61

    Alignment length:33
                                    32        42        52   
         A0A0H3CFC9_C    23 RQQAIGVKLRQMFDEVVNEPVPDEFLAILRKAE  55
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 3t0y B  30 RQQAIGVKLRQmFDEVVNEPVPDEFLAILRKAE  62
                                    39 |      49        59   
                                      41-MSE

Chain B from PDB  Type:PROTEIN  Length:33
 aligned with Q9A2T0_CAUCR | Q9A2T0 from UniProtKB/TrEMBL  Length:68

    Alignment length:33
                                    39        49        59   
         Q9A2T0_CAUCR    30 RQQAIGVKLRQMFDEVVNEPVPDEFLAILRKAE  62
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 3t0y B  30 RQQAIGVKLRQmFDEVVNEPVPDEFLAILRKAE  62
                                    39 |      49        59   
                                      41-MSE

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with A0A0H3CBZ6_C | A0A0H3CBZ6 from UniProtKB/TrEMBL  Length:266

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
         A0A0H3CBZ6_C     1 MSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSSGAQLEVGHDQGLHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELAT 141
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0y C  15 mSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSS-------------AGDDAAQRLmRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELAT 142
                            |       24        34        44        54        64        74      |  -         -|       91       101       111       121       131       141 
                           15-MSE                                                            81            82       91-MSE

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with Q9A2S9_CAUCR | Q9A2S9 from UniProtKB/TrEMBL  Length:266

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
         Q9A2S9_CAUCR     1 MSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSSGAQLEVGHDQGLHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELAT 141
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0y C  15 mSLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANLSPRVALYRVFHAIWLSS-------------AGDDAAQRLmRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELAT 142
                            |       24        34        44        54        64        74      |  -         -|       91       101       111       121       131       141 
                           15-MSE                                                            81            82       91-MSE

Chain D from PDB  Type:PROTEIN  Length:32
 aligned with A0A0H3CFC9_C | A0A0H3CFC9 from UniProtKB/TrEMBL  Length:61

    Alignment length:32
                                    32        42        52  
         A0A0H3CFC9_C    23 RQQAIGVKLRQMFDEVVNEPVPDEFLAILRKA  54
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 3t0y D  30 RQQAIGVKLRQmFDEVVNEPVPDEFLAILRKA  61
                                    39 |      49        59  
                                      41-MSE

Chain D from PDB  Type:PROTEIN  Length:32
 aligned with Q9A2T0_CAUCR | Q9A2T0 from UniProtKB/TrEMBL  Length:68

    Alignment length:32
                                    39        49        59  
         Q9A2T0_CAUCR    30 RQQAIGVKLRQMFDEVVNEPVPDEFLAILRKA  61
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 3t0y D  30 RQQAIGVKLRQmFDEVVNEPVPDEFLAILRKA  61
                                    39 |      49        59  
                                      41-MSE

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 3T0Y)

(no "CATH Domain" information available for 3T0Y)

(no "Pfam Domain" information available for 3T0Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (A0A0H3CBZ6_C | A0A0H3CBZ6)

Chain A,C (Q9A2S9_CAUCR | Q9A2S9)

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:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain B,D (Q9A2T0_CAUCR | Q9A2T0)

Chain B,D (A0A0H3CFC9_C | A0A0H3CFC9)

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 3t0y)

	Cis Peptide Bonds
		Ala C:82 - Gly C:83	[ RasMol ]

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	3t0y
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	A0A0H3CBZ6_C \| A0A0H3CBZ6
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	Q9A2S9_CAUCR \| Q9A2S9
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	Q9A2T0_CAUCR \| Q9A2T0
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	A0A0H3CBZ6_C \| A0A0H3CBZ6
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	Q9A2S9_CAUCR \| Q9A2S9
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UniProtKB/TrEMBL
	Q9A2S9_CAUCR \| Q9A2S9	:	3n0r

(no "Related Entries Specified in the PDB File" available for 3T0Y)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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