4G8X - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   G1 ORF67 / STAPHYLOCCUS AUREUS SIGMAA DOMAIN 4 COMPLEX

Authors :   S. A. Darst, J. S. Osmundson, C. M. Montero-Diaz, A. Hochschild

Date :   23 Jul 12 (Deposition) - 07 Aug 13 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Rnap Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osmundson, C. Montero-Diez, L. F. Westblade, A. Hochschild, S. A. Darst
Promoter-Specific Transcription Inhibition In Staphylococcu Aureus By A Phage Protein.
Cell(Cambridge, Mass. ) V. 151 1005 2012
PubMed-ID: 23178120 | Reference-DOI: 10.1016/J.CELL.2012.10.034

Molecule 1 - RNA POLYMERASE SIGMA FACTOR RPOD
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 296-357
	Gene	:	PLAC, RPOD, SAOUHSC_01662, SIGA, SIGMA A DOMAIN 4
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	93061
	Strain	:	NCTC 8325

Molecule 2 - ORF067
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ORF67
	Organism Scientific	:	STAPHYLOCOCCUS PHAGE G1
	Organism Taxid	:	292029

		1	2	3	4
Asymmetric Unit	:	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, 9)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 4G8X)

(no "SS Bond" information available for 4G8X)

Asymmetric Unit

No.	Residues
1	Asn B:91	-	Pro B:92
2	Lys B:148	-	Thr B:149
3	Lys B:159	-	Ser B:160
4	Leu C:304	-	Asp C:305
5	Asp C:309	-	Arg C:310
6	Phe C:319	-	Gly C:320
7	Lys C:334	-	Val C:335
8	Val C:335	-	Phe C:336
9	Ala D:31	-	Asn D:32
10	Thr D:114	-	Glu D:115
11	Glu D:115	-	Glu D:116
12	Glu D:150	-	Glu D:151
13	Lys D:170	-	Glu D:171

(no "SAP(SNP)/Variant" information available for 4G8X)

(no "PROSITE Motif" information available for 4G8X)

(no "Exon" information available for 4G8X)

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:61
                                                                                             
               SCOP domains d4g8xa_ A: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 4g8x A 296 mKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 356
                            |      305       315       325       335       345       355 
                            |                                                            
                          296-MSE

Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eeeeeee...eeeeeeee..............eeeee.....eeeeee..............hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8x B   1 mKLKILDKDNATLNVFHRNKEHKTIDNVPTANLVDWYPLSNAYEYKLSRNGEYLELKRLRSTLPSSYGLDDNNQDIIRDNNHRCKIGYWYNPAVRKDNLKIIEKAKQYGLPIITEEYDANTVEQGFRDIGVIFQSLKTIVVTRYLEGKTEEELRIFNmKSEESQLNEALKESDFSVDLTYSDLGQIYNmLLLmKKIS 197
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  |    
                            1-MSE                                                                                                                                                      158-MSE                        189-MSE    
                                                                                                                                                                                                                          193-MSE

Chain C from PDB  Type:PROTEIN  Length:54
                                                                                      
               SCOP domains d4g8xc_ C: automated matches                           SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh.........hhhhhh.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 4g8x C 302 DVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGTRERIRQIEAKALRKLRH 356
                                   311       321       331     ||342       352    
                                                             337|                 
                                                              339

Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eee...........hhhhh.....ee..ee...............................hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8x D   1 mKLKILDKDNATLNVFTIDNVPTANLVDWYPLSNAYEYLKRLRSTLPSSYGLDDNNQDIIRDNNHRCGYWYNPAVRKDNLKIIEKAKQYGLPIITEEYDANTVEQGFRDIGVIFQSLKTIVVTRYLEGKTEEELRIFNmKSEESQLNEALKESSVDLTYSDLGQIYNmLLLmKKISK 198
                            |       10     || 27        37       |57        67        77      ||89        99       109       119       129       139       149       159       169  ||   181       191 |     
                            1-MSE         16|                   45|                          84|                                                                    158-MSE       172|           189-MSE     
                                           24                    56                           87                                                                                   175               193-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 '\|'

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: automated matches (3)

Staphylococcus aureus [TaxId: 93061] (3)

1a	d4g8xa_	A:
1b	d4g8xc_	C:

(no "CATH Domain" information available for 4G8X)

(no "Pfam Domain" information available for 4G8X)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
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		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
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	Ligands, Modified Residues, Ions
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 4g8x)

	Cis Peptide Bonds
		Ala D:31 - Asn D:32	[ RasMol ]
		Asn B:91 - Pro B:92	[ RasMol ]
		Asp C:309 - Arg C:310	[ RasMol ]
		Glu D:115 - Glu D:116	[ RasMol ]
		Glu D:150 - Glu D:151	[ RasMol ]
		Leu C:304 - Asp C:305	[ RasMol ]
		Lys B:148 - Thr B:149	[ RasMol ]
		Lys B:159 - Ser B:160	[ RasMol ]
		Lys C:334 - Val C:335	[ RasMol ]
		Lys D:170 - Glu D:171	[ RasMol ]
		Phe C:319 - Gly C:320	[ RasMol ]
		Thr D:114 - Glu D:115	[ RasMol ]
		Val C:335 - Phe C:336	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
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Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4g8x
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
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Access by UniProt ID/Accession number
	Q4Z9Y5_9CAUD \| Q4Z9Y5
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		Genomic Information	:	Ensembl
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		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	SIGA_STAA8 \| P0A0J0
		Comparative Protein Structure Models	:	ModBase
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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	Q4Z9Y5_9CAUD \| Q4Z9Y5
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	SIGA_STAA8 \| P0A0J0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SIGA_STAA8 \| P0A0J0	:	4g6d 4g94
UniProtKB/TrEMBL
	Q4Z9Y5_9CAUD \| Q4Z9Y5	:	4g6d 4g94

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File