1S77 | PH0010 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   T7 RNAP PRODUCT PYROPHOSPHATE ELONGATION COMPLEX

Authors :   Y. W. Yin, T. A. Steitz

Date :   29 Jan 04 (Deposition) - 23 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.69

Chains :   Asym./Biol. Unit : D,N,R,T

Keywords :   T7 Rna Polymerase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. W. Yin, T. A. Steitz
The Structural Mechanism Of Translocation And Helicase Activity In T7 Rna Polymerase.
Cell(Cambridge, Mass. ) V. 116 393 2004
PubMed-ID: 15016374 | Reference-DOI: 10.1016/S0092-8674(04)00120-5
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(GPCPCPGPTPGPCPGPCPAPTPTPCPGPCPCPGPTPGP TPT)-3')**
	Chains	:	T
	Engineered	:	YES
	Other Details	:	DNA OLIGOMER IS SYNTHESIZED
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(TPTPTPAPCPGPTPTPGPCPGPCPAPCPGPGPC)-3')**
	Chains	:	N
	Engineered	:	YES
	Other Details	:	DNA OLIGOMER IS SYNTHESIZED
	Synthetic	:	YES

*Molecule 3 - RNA (5'-R(APCPAPCPGPGPCPGPAP(3DA))-3')*
	Chains	:	R
	Engineered	:	YES
	Other Details	:	RNA OLIGOMER IS SYNTHESIZED
	Synthetic	:	YES

Molecule 4 - DNA-DIRECTED RNA POLYMERASE
	Chains	:	D
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	1
	Organism Scientific	:	ENTEROBACTERIA PHAGE T7
	Organism Taxid	:	10760

		1	2	3	4
Asymmetric/Biological Unit	:	D	N	R	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	3DA	1	Mod. Nucleotide	3'-DEOXYADENOSINE-5'-MONOPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	3DA R:1 , A R:2	BINDING SITE FOR RESIDUE MG R 902
2	AC2	SOFTWARE	ASP D:537 , GLY D:538 , ASP D:812 , POP D:901 , HOH D:904 , 3DA R:1	BINDING SITE FOR RESIDUE MG D 903
3	AC3	SOFTWARE	LYS D:472 , ASP D:537 , GLY D:538 , SER D:539 , CYS D:540 , TYR D:571 , ARG D:627 , LYS D:631 , MG D:903 , HOH D:904	BINDING SITE FOR RESIDUE POP D 901

(no "SS Bond" information available for 1S77)

(no "Cis Peptide Bond" information available for 1S77)

(no "SAP(SNP)/Variant" information available for 1S77)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNA_POL_PHAGE_1	PS00900	Bacteriophage-type RNA polymerase family active site signature 1.	RPOL_BPT7	533-544	1	D:533-544
2	RNA_POL_PHAGE_2	PS00489	Bacteriophage-type RNA polymerase family active site signature 2.	RPOL_BPT7	625-639	1	D:625-639

(no "Exon" information available for 1S77)

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 D from PDB  Type:PROTEIN  Length:828
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:872
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881  
            RPOL_BPT7    12 SDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
               SCOP domains d1s77d_ D: T7 RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1s77D01 D:12-325 T7 RNA polymerase, domain 1                                                                                                                                                                                                                                                                              1s77D02 D:326-411  [code=1.10.287.26               0, no name defined]                ---------1s77D03                      1s77D04 D:450-527  [code=1.10.287.280, no name defined]                       1s77D03                   1s77D05 D:554-784 5' to 3' exonuclease, C              -terminal subdomain                                                                                                                                                             1s77D03 D:421-449,D:528-553,D:785-872  [code=3.30.70.370, no name defined]              ----------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------     -------------------------------          -------------------------------------------------------------------------------------------------------------------------               ------------------------------------------------------------------------RNA_pol-1s77D01 D:449-883                                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......................hhhhhh.hhhhhh.....-----.......hhhhhhhhhhhhhhhh....ee..----------....eehhhhhhhhhhhhhhhhh.................................ee..hhhhhhhhh...hhhhhhhhhhhhh..eeehhhhhhhhhhhh...................---------------......hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee........hhhhhhheee...eehhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhh...ee...eeee..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.....--------------.....hhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.ee......eee....eeee.....eeee.........eee...eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s77 D  12 SDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKG-----AWSSWHKEDSIHVGVRCIEMLIESTGMVSLH----------SETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELP---------------WKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEV--------------VKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  |    201       211       221        |-       241       251       261       271       281       291       301       311       321       331       341       351       361         -     | 381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591  |      -       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881  
                                                                                                                                                                                                                194   200                           230        241                                                                                                                     361             377                                                                                                                                                                                                                      594            609

Chain N from PDB  Type:DNA  Length:17
                                                 
                 1s77 N  14 TTTACGTTGCGCACGGC  30
                                    23

Chain R from PDB  Type:RNA  Length:10
                                          
                 1s77 R  10 ACACGGCGAa   1
                            |||||||||1
                           10||||||||1-3DA
                             9||||||| 
                              8|||||| 
                               7||||| 
                                6|||| 
                                 5||| 
                                  4|| 
                                   3| 
                                    2

Chain T from PDB  Type:DNA  Length:21
                                                     
                 1s77 T 130 GCCGTGCGCATTCGCCGTGTT 110
                            |||||||121|||||||111|
                            ||||||122||||||113|||
                          130||||||121||||||112||
                           129||||||120||||||111|
                            128||||| 119||||| 110
                             127||||  118||||    
                              126|||   117|||    
                               125||    116||    
                                124|     115|    
                                 123      114

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: T7 RNA polymerase (12)

Protein domain: T7 RNA polymerase (11)

Bacteriophage T7 [TaxId: 10760] (11)

d1s77d_

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RNA_pol] (7)

Family: RNA_pol (7)

Enterobacteria phage T7 (Bacteriophage T7) (7)

RNA_pol-1s77D01

D:449-883

Asymmetric/Biological Unit(hide GO term definitions)

Chain D (RPOL_BPT7 | P00573)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0039695	DNA-templated viral transcription	A transcription process that uses a viral DNA as a template.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		3DA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		POP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s77)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
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
	1s77
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RPOL_BPT7 \| P00573
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.7.6
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RPOL_BPT7 \| P00573
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RPOL_BPT7 \| P00573	:	1aro 1cez 1h38 1msw 1qln 1s0v 1s76 2pi4 2pi5 3e2e 3e3j 4rnp

(no "Related Entries Specified in the PDB File" available for 1S77)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (5, 5)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File