ECOD: domain e1y1vB5

Domain ID e1y1vB5

A: a+b complex topology
X: barrel domain in beta subunit of DNA dependent RNA-polymerase
H: barrel domain in beta subunit of DNA dependent RNA-polymerase
T: barrel domain in beta subunit of DNA dependent RNA-polymerase
F: RNA_pol_Rpb2_6,RNA_pol_Rpb2_5

UID:	001511448
Type:	Automatic domain
Parent:	e4by7B4
Range:	B:631-813
PDB:	1y1v
PDB Description:	DNA-directed RNA polymerase II 140 kDa polypeptide
UniProt:	P08518
Hsap BLAST neighbor:	P30876
Species:	Saccharomyces cerevisiae

Domains in the same chain:

Download Pymol

e1y1vB7	B:20-70,B:90-134,B:164-218,B:405-541	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	N-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1y1vB6	B:219-404	insertion domain in beta subunit of DNA dependent RNA-polymerase	insertion domain in beta subunit of DNA dependent RNA-polymerase	insertion domain in beta subunit of DNA dependent RNA-polymerase
e1y1vB3	B:542-630	inserted a+b domain in yeast RNA polymerase beta subunit	inserted a+b domain in yeast RNA polymerase beta subunit	inserted a+b domain in yeast RNA polymerase beta subunit
e1y1vB5	B:631-813	barrel domain in beta subunit of DNA dependent RNA-polymerase	barrel domain in beta subunit of DNA dependent RNA-polymerase	barrel domain in beta subunit of DNA dependent RNA-polymerase
e1y1vB2	B:814-850,B:975-1097	cradle loop barrel	RIFT-related	double psi
e1y1vB1	B:851-974	alpha/beta-Hammerhead/Barrel-sandwich hybrid	alpha/beta-Hammerhead/Barrel-sandwich hybrid	Single hybrid motif
e1y1vB4	B:1098-1224	C-terminal domain in beta subunit of DNA dependent RNA-polymerase	C-terminal domain in beta subunit of DNA dependent RNA-polymerase	C-terminal domain in beta subunit of DNA dependent RNA-polymerase

Domains in the same PDB:

Structural contacts of domain e1y1vB5 of H-group "barrel domain in beta subunit of DNA dependent RNA-polymerase":

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The domain and its neighboring domains (both within the asymmetric unit and to crystallographic symmetry mates) are represented by spheres and linked by lines. Distances between the center of the domain and interfaces are shown for each contact.

Domain ID	Symmetry operator	H-group	Visualization
e1y1vA3	B:x,y,z->A:X,Y,Z	second helical domain in RNA-polymerase beta-prime subunit	Interaction Interface Pymol
e1y1vC3	B:X,Y,Z->C:x,y,z	Insert subdomain of RNA polymerase alpha subunit	Interaction Interface Pymol
e1y1vJ1	B:X,Y,Z->J:x,y,z	RPB10	Interaction Interface Pymol
e1y1vI4	B:X,Y,Z->I:x,y,z	Rubredoxin-related	Interaction Interface Pymol

e1y1vA4	A:2-336	N-terminal domain in RNA-polymerase beta-prime subunit	N-terminal domain in RNA-polymerase beta-prime subunit	N-terminal domain in RNA-polymerase beta-prime subunit
e1y1vA5	A:337-374,A:436-519	cradle loop barrel	RIFT-related	double psi
e1y1vA2	A:375-435	MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase
e1y1vA9	A:520-662	first helical domain in RNA-polymerase beta-prime subunit	first helical domain in RNA-polymerase beta-prime subunit	first helical domain in RNA-polymerase beta-prime subunit
e1y1vA3	A:663-871	second helical domain in RNA-polymerase beta-prime subunit	second helical domain in RNA-polymerase beta-prime subunit	second helical domain in RNA-polymerase beta-prime subunit
e1y1vA7	A:872-1059	helical domain in yeast RNA-polymerases	third helical domain in yeast RNA-polymerase II beta-prime subunit	third helical domain in yeast RNA-polymerase II beta-prime subunit
e1y1vA1	A:1060-1102,A:1301-1455	central helical domain in RNA-polymerase beta-prime subunit	central helical domain in RNA-polymerase beta-prime subunit	central helical domain in RNA-polymerase beta-prime subunit
e1y1vA6	A:1103-1131,A:1243-1300	ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e1y1vA8	A:1132-1242	permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e1y1vB7	B:20-70,B:90-134,B:164-218,B:405-541	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	N-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1y1vB6	B:219-404	insertion domain in beta subunit of DNA dependent RNA-polymerase	insertion domain in beta subunit of DNA dependent RNA-polymerase	insertion domain in beta subunit of DNA dependent RNA-polymerase
e1y1vB3	B:542-630	inserted a+b domain in yeast RNA polymerase beta subunit	inserted a+b domain in yeast RNA polymerase beta subunit	inserted a+b domain in yeast RNA polymerase beta subunit
e1y1vB5	B:631-813	barrel domain in beta subunit of DNA dependent RNA-polymerase	barrel domain in beta subunit of DNA dependent RNA-polymerase	barrel domain in beta subunit of DNA dependent RNA-polymerase
e1y1vB2	B:814-850,B:975-1097	cradle loop barrel	RIFT-related	double psi
e1y1vB1	B:851-974	alpha/beta-Hammerhead/Barrel-sandwich hybrid	alpha/beta-Hammerhead/Barrel-sandwich hybrid	Single hybrid motif
e1y1vB4	B:1098-1224	C-terminal domain in beta subunit of DNA dependent RNA-polymerase	C-terminal domain in beta subunit of DNA dependent RNA-polymerase	C-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1y1vC2	C:3-41,C:173-268	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e1y1vC3	C:42-172	Ribosomal protein TL5/L25 C-terminal domain-like	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit
e1y1vD1	D:4-71,D:131-221	HhH/H2TH	SAM/DNA-glycosylase	SAM domain-like
e1y1vE2	E:2-142	Restriction endonuclease-like	Eukaryotic RPB5 N-terminal domain	Eukaryotic RPB5 N-terminal domain
e1y1vE1	E:143-215	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit
e1y1vF1	F:72-155	RPB6/omega subunit-like	RPB6/omega subunit-like	RPB6
e1y1vG4	G:1-68	Dodecin subunit-like	Flavin-binding protein dodecin-like	Flavin-binding protein dodecin-like
e1y1vG3	G:69-171	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e1y1vH1	H:2-146	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e1y1vI3	I:2-49	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related
e1y1vI4	I:50-120	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related
e1y1vJ1	J:1-65	HTH	RPB10	RPB10
e1y1vK1	K:1-114	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e1y1vL1	L:25-70	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related
e1y1vS1	S:136-255	RuvA-C	Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	Elongation factor TFIIS domain 2/ Kix domain of creb binding protein
e1y1vS2	S:256-309	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related