ECOD: domain e2pmzA5

Domain ID e2pmzA5

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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:	001117600
Type:	Manual and representative domain
Range:	A:645-879
PDB:	2pmz
PDB Description:	DNA-directed RNA polymerase subunit A
UniProt:	Q980R2
Hsap BLAST neighbor:	P24928
Species:

Domains in the same chain:

e2pmzA1	A:4-306	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
e2pmzA2	A:307-347,A:411-494	cradle loop barrel	RIFT-related	double psi
e2pmzA3	A:348-410	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
e2pmzA4	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
e2pmzA5	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:

e2pmzA1	A:4-306	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
e2pmzA2	A:307-347,A:411-494	cradle loop barrel	RIFT-related	double psi
e2pmzA3	A:348-410	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
e2pmzA4	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
e2pmzA5	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
e2pmzB4	B:5-167,B:342-472	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
e2pmzB2	B:168-341	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
e2pmzB1	B:473-572	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
e2pmzB7	B:573-712	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
e2pmzB3	B:713-749,B:873-995	cradle loop barrel	RIFT-related	double psi
e2pmzB6	B:750-872	alpha/beta-Hammerhead/Barrel-sandwich hybrid	alpha/beta-Hammerhead/Barrel-sandwich hybrid	Single hybrid motif
e2pmzB5	B:996-1119	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
e2pmzC2	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
e2pmzC1	C:66-146,C:238-395	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
e2pmzD1	D:2-36,D:159-265	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2pmzD2	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
e2pmzE2	E:1-78	Dodecin subunit-like	Flavin-binding protein dodecin-like	Flavin-binding protein dodecin-like
e2pmzE1	E:79-180	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e2pmzF1	F:1-89	HhH/H2TH	SAM/DNA-glycosylase	SAM domain-like
e2pmzG2	G: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
e2pmzG1	G:66-146,G:238-395	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
e2pmzH1	H:9-82	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit
e2pmzK1	K:11-92	RPB6/omega subunit-like	RPB6/omega subunit-like	RPB6
e2pmzL1	L:1-92	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2pmzN1	N:1-64	HTH	RPB10	RPB10
e2pmzP1	P:6-48	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related
e2pmzQ3	Q:4-96,Q:174-306	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
e2pmzQ5	Q:307-347,Q:411-494	cradle loop barrel	RIFT-related	double psi
e2pmzQ2	Q:348-410	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
e2pmzQ1	Q: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
e2pmzQ4	Q: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
e2pmzR6	R:5-167,R:342-472	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
e2pmzR3	R:168-341	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
e2pmzR1	R:473-572	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
e2pmzR2	R:573-712	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
e2pmzR4	R:713-749,R:873-995	cradle loop barrel	RIFT-related	double psi
e2pmzR7	R:750-872	alpha/beta-Hammerhead/Barrel-sandwich hybrid	alpha/beta-Hammerhead/Barrel-sandwich hybrid	Single hybrid motif
e2pmzR5	R:996-1119	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
e2pmzS1	S:2-36,S:159-265	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2pmzS2	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
e2pmzT2	T:1-78	Dodecin subunit-like	Flavin-binding protein dodecin-like	Flavin-binding protein dodecin-like
e2pmzT1	T:79-180	OB-fold	Nucleic acid-binding proteins	Nucleic acid-binding proteins
e2pmzU1	U:1-89	HhH/H2TH	SAM/DNA-glycosylase	SAM domain-like
e2pmzV1	V:9-82	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit
e2pmzW1	W:11-92	RPB6/omega subunit-like	RPB6/omega subunit-like	RPB6
e2pmzX1	X:1-92	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11-like subunits of RNA polymerase
e2pmzY1	Y:1-64	HTH	RPB10	RPB10
e2pmzZ1	Z:6-48	Rubredoxin-like	Rubredoxin-related	Rubredoxin-related

Structural contacts of domain e2pmzA5 of H-group "second helical domain in RNA-polymerase beta-prime subunit":

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
e2pmzB1	A:X,Y,Z->B:x,y,z	inserted a+b domain in yeast RNA polymerase beta subunit	Interaction Interface Pymol
e2pmzB4	A:X,Y,Z->B:x,y,z	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2pmzB3	A:X,Y,Z->B:x,y,z	RIFT-related	Interaction Interface Pymol
e2pmzB2	A:X,Y,Z->B:x,y,z	insertion domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2pmzB5	A:X,Y,Z->B:x,y,z	C-terminal domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2pmzB7	A:X,Y,Z->B:x,y,z	barrel domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2pmzC1	A:X,Y,Z->C:x,y,z	central helical domain in RNA-polymerase beta-prime subunit	Interaction Interface Pymol
e2pmzC2	A:X,Y,Z->C:x,y,z	third helical domain in yeast RNA-polymerase II beta-prime subunit	Interaction Interface Pymol
e2pmzK1	A:X,Y,Z->K:x,y,z	RPB6/omega subunit-like	Interaction Interface Pymol
e2pmzR6	A:X,Y,Z->R:x,y,z	N-terminal domain in beta subunit of DNA dependent RNA-polymerase	Interaction Interface Pymol
e2pmzH1	A:X,Y,Z->H:x,y,z	RPB5-like RNA polymerase subunit	Interaction Interface Pymol
e2pmzD1	A:X,Y,Z->D:x,y,z	RBP11-like subunits of RNA polymerase	Interaction Interface Pymol