ECOD: domain e2y0sA2

Domain ID e2y0sA2

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A: a+b complex topology
X: second helical domain in RNA-polymerase beta-prime subunit
H: second helical domain in RNA-polymerase beta-prime subunit
T: second helical domain in RNA-polymerase beta-prime subunit
F: RNA_pol_Rpb1_5,RNA_pol_Rpb1_4

UID:	001711687
Type:	Automatic domain
Parent:	e1twfA10
Range:	A:645-879
PDB:	2y0s
PDB Description:	DNA-DIRECTED RNA POLYMERASE
UniProt:	B8YB53
Hsap BLAST neighbor:	P24928
Species:	Sulfolobus shibatae

Domains in the same chain:

e2y0sA1	A:4-151,A:175-306	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
e2y0sA3	A:307-494	cradle loop barrel	RIFT-related	double psi
e2y0sA4	A:495-644	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
e2y0sA2	A:645-879	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

Domains in the same PDB:

e2y0sA1	A:4-151,A:175-306	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
e2y0sA3	A:307-494	cradle loop barrel	RIFT-related	double psi
e2y0sA4	A:495-644	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
e2y0sA2	A:645-879	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
e2y0sB6	B:8-170,B:345-475	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
e2y0sB1	B:171-344	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
e2y0sB7	B:476-575	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
e2y0sB2	B:576-715	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
e2y0sB4	B:716-752,B:876-998	cradle loop barrel	RIFT-related	double psi
e2y0sB5	B:753-875	alpha/beta-Hammerhead/Barrel-sandwich hybrid	alpha/beta-Hammerhead/Barrel-sandwich hybrid	Single hybrid motif
e2y0sB3	B:999-1122	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
e2y0sC3	C:11-65	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
e2y0sC2	C:66-115,C:276-395	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
e2y0sC4	C:116-147,C:233-275	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
e2y0sC1	C:148-232	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
e2y0sD1	D:2-36,D:159-264	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2y0sD2	D:37-158	Ribosomal protein TL5/L25 C-terminal domain-like	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit
e2y0sE4	E:1-66	Dodecin subunit-like	Flavin-binding protein dodecin-like	Flavin-binding protein dodecin-like
e2y0sE3	E:67-170	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e2y0sF1	F:3-92	HhH/H2TH	SAM/DNA-glycosylase	SAM domain-like
e2y0sG1	G:7-116	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e2y0sH1	H:9-82	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit
e2y0sI1	I:11-92	RPB6/omega subunit-like	RPB6/omega subunit-like	RPB6
e2y0sJ1	J:39-77	YqgQ-like	YqgQ-like	YqgQ-like
e2y0sK1	K:11-92	RPB6/omega subunit-like	RPB6/omega subunit-like	RPB6
e2y0sL1	L:1-91	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2y0sM1	M:1-91	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2y0sN1	N:1-64	HTH	RPB10	RPB10
e2y0sO1	O:1-64	HTH	RPB10	RPB10
e2y0sP1	P:4-48	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related
e2y0sQ1	Q:39-77	YqgQ-like	YqgQ-like	YqgQ-like
e2y0sR2	R:8-170,R:345-475	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
e2y0sR5	R:171-344	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
e2y0sR7	R:476-575	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
e2y0sR6	R:576-715	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
e2y0sR1	R:716-752,R:876-998	cradle loop barrel	RIFT-related	double psi
e2y0sR4	R:753-875	alpha/beta-Hammerhead/Barrel-sandwich hybrid	alpha/beta-Hammerhead/Barrel-sandwich hybrid	Single hybrid motif
e2y0sR3	R:999-1122	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
e2y0sS1	S:2-36,S:159-264	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2y0sS2	S:37-158	Ribosomal protein TL5/L25 C-terminal domain-like	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit
e2y0sT4	T:1-66	Dodecin subunit-like	Flavin-binding protein dodecin-like	Flavin-binding protein dodecin-like
e2y0sT3	T:67-170	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e2y0sU1	U:3-92	HhH/H2TH	SAM/DNA-glycosylase	SAM domain-like
e2y0sV1	V:7-116	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e2y0sW2	W:4-151,W:175-306	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
e2y0sW3	W:307-494	cradle loop barrel	RIFT-related	double psi
e2y0sW1	W:495-644	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
e2y0sW4	W:645-879	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
e2y0sX1	X:4-48	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related
e2y0sY1	Y:11-65	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
e2y0sY3	Y:66-115,Y:276-395	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
e2y0sY4	Y:116-147,Y:233-275	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
e2y0sY2	Y:148-232	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
e2y0sZ1	Z:9-82	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit

Structural contacts of domain e2y0sA2 of H-group "second helical domain in RNA-polymerase beta-prime subunit":

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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
e2y0sB3	A:X,Y,Z->B:x,y,z	C-terminal domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2y0sB2	A:X,Y,Z->B:x,y,z	barrel domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2y0sB1	A:X,Y,Z->B:x,y,z	insertion domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2y0sB6	A:X,Y,Z->B:x,y,z	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2y0sB4	A:X,Y,Z->B:x,y,z	RIFT-related	Interaction Interface Pymol
e2y0sC3	A:X,Y,Z->C:x,y,z	third helical domain in yeast RNA-polymerase II beta-prime subunit	Interaction Interface Pymol
e2y0sC2	A:X,Y,Z->C:x,y,z	central helical domain in RNA-polymerase beta-prime subunit	Interaction Interface Pymol
e2y0sG1	A:X,Y,Z->G:x,y,z	Nucleic acid-binding proteins	Interaction Interface Pymol
e2y0sK1	A:X,Y,Z->K:x,y,z	RPB6/omega subunit-like	Interaction Interface Pymol
e2y0sH1	A:X,Y,Z->H:x,y,z	RPB5-like RNA polymerase subunit	Interaction Interface Pymol
e2y0sR2	A:x,y,z->R:-X,Y-1/2,-Z+1	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2y0sV1	A:X,Y,Z->V:x,y,z	Nucleic acid-binding proteins	Interaction Interface Pymol