NPIDB: 2R92 structure

General information

PDB ID

2R92

Title

ELONGATION COMPLEX OF RNA POLYMERASE II WITH ARTIFICIAL RDRP SCAFFOLD

PDB header

TRANSFERASE/RNA

Date

2007-09-12

Experimental method

X-RAY DIFFRACTION

Resolution (A)

3.8

Kind

rna

Organism

SACCHAROMYCES CEREVISIAE


Download complex	View in Jmol

Quick Links

PDB	PDBe	MMDB	Jena	OCA
CATH	PDBsum	HSSP	PDBePISA	UniProt
ProteopediA	BIPA
	PRIDB

Composition of PDB entry and biounits
File:	Protein chains:	DNA chains:	RNA chains:	No. of models:	Action:

PDB entry:

pdb2r92.pdb	ABCDEFGHIJKL		PT	0

Biounits:

2r92.pdb1.pdb	ABCDEFGHIJKL		PT	1

Pfam domains
Name:	Type:	Domain:	E-value:	Significance:	Clan:	Prot. chain:	Start res.:	End res.:	Nuc. chains:	Int. mode:	Action:

RNA_pol_Rpb1_1	Domain	P04050_11-340	2.7e-115	1	No_clan	A	11	340	PT
RNA_pol_Rpb1_5	Domain	P04050_807-1397	1.6e-93	1	No_clan	A	807	1397	T
RNA_pol_Rpb1_2	Domain	P04050_342-507	1.7e-77	1	No_clan	A	342	507	T
RNA_pol_Rpb1_6	Domain	P04050_873-1056	2.4e-63	1	No_clan	A	873	1056
RNA_pol_Rpb1_3	Domain	P04050_510-669	7.9e-47	1	No_clan	A	510	669
RNA_pol_Rpb1_7	Domain	P04050_1141-1274	2.2e-38	1	No_clan	A	1141	1274
RNA_pol_Rpb1_4	Domain	P04050_693-800	5.3e-35	1	No_clan	A	693	800
RNA_pol_Rpb2_6	Domain	P08518_752-1124	7.5e-122	1	CL0410	B	752	1124	PT
RNA_pol_Rpb2_2	Domain	P08518_219-407	2.3e-51	1	No_clan	B	219	407
RNA_pol_Rpb2_7	Domain	P08518_1126-1219	1.7e-33	1	No_clan	B	1126	1219
RNA_pol_Rpb2_4	Domain	P08518_580-641	1.5e-25	1	No_clan	B	580	641
RNA_pol_Rpb2_3	Domain	P08518_481-545	9.3e-20	1	No_clan	B	481	545
RNA_pol_Rpb2_5	Domain	P08518_681-745	1.4e-19	1	No_clan	B	681	745
RNA_pol_A_bac	Domain	P16370_49-171	7.3e-32	1	No_clan	C	49	171
RNA_pol_L	Domain	P16370_19-255	6.7e-19	1	CL0509	C	19	255
RNA_pol_Rpb5_C	Domain	P20434_142-214	1.6e-31	1	No_clan	E	142	214
RNA_pol_Rpb5_N	Domain	P20434_6-100	1.1e-29	1	CL0236	E	6	100
S1	Domain	P34087_80-161	6.2e-18	1	CL0021	G	80	161
SHS2_Rpb7-N	Domain	P34087_8-79	2.6e-16	1	CL0319	G	8	79
RNA_POL_M_15KD	Domain	P27999_4-41	1.2e-17	1	CL0167	I	4	41
TFIIS_C	Domain	P27999_73-111	0.000000000000013	1	CL0167	I	73	111
RNA_pol_N	Domain	P22139_1-60	5.4e-30	1	No_clan	J	1	60
RNA_pol_L_2	Domain	P38902_30-104	1.5e-24	1	CL0509	K	30	104
DNA_RNApol_7kD	Domain	P40422_29-60	1.9e-16	1	CL0167	L	29	60
RNA_pol_Rpb2_1	Family	P08518_42-455	8.5e-54	1	No_clan	B	42	455
RNA_pol_Rpb4	Family	P20433_49-218	8.6e-39	1	CL0426	D	49	218
RNA_pol_Rpb6	Family	P20435_79-132	8.3e-18	1	No_clan	F	79	132
RNA_pol_Rpb8	Family	P20436_7-146	3e-43	1	CL0021	H	7	146

SCOP domains
Classification:	Protein:	Prot. chain:	Start res.:	End res.:	Nuc. chains:	Int. mode:	Action:

Class: Low resolution protein structures Fold: RNA polymerase Superfamily: RNA polymerase Family: RNA polymerase	Complete 12-subunit RNA polymerase II complex	A	2	1455	PT	-
Class: Multi-domain proteins (alpha and beta) Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase Family: RNA-polymerase beta	RBP2	B	20	1224	PT	-
Class: Low resolution protein structures Fold: RNA polymerase Superfamily: RNA polymerase Family: RNA polymerase	Complete 12-subunit RNA polymerase II complex	D	4	221		-
Class: All alpha proteins Fold: RPB6/omega subunit-like Superfamily: RPB6/omega subunit-like Family: RPB6	RPB6	F	72	155		-
Class: Low resolution protein structures Fold: RNA polymerase Superfamily: RNA polymerase Family: RNA polymerase	Complete 12-subunit RNA polymerase II complex	G	1	171		-
Class: All beta proteins Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: RNA polymerase subunit RBP8	RNA polymerase subunit RBP8	H	2	146		-
Class: All alpha proteins Fold: DNA/RNA-binding 3-helical bundle Superfamily: RNA polymerase subunit RPB10 Family: RNA polymerase subunit RPB10	RNA polymerase subunit RPB10	J	1	65		-
Class: Low resolution protein structures Fold: RNA polymerase Superfamily: RNA polymerase Family: RNA polymerase	Complete 12-subunit RNA polymerase II complex	K	1	112		-
Class: Small proteins Fold: Rubredoxin-like Superfamily: RNA polymerase subunits Family: RBP12 subunit of RNA polymerase II	RBP12 subunit of RNA polymerase II	L	25	70		-

GO terms
Protein chains:	GO type:	GO description:
B=1-1224	C	mitochondrion
B=1-1224	F	ribonucleoside binding
C=1-318	P	termination of RNA polymerase II transcription
D=1-221	F	nucleotide binding
D=1-221	P	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D=1-221	P	mRNA export from nucleus in response to heat stress
D=1-221	P	recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
D=1-221	P	DNA repair
E=1-215	P	tRNA transcription from RNA polymerase III promoter
F=1-155	C	cytoplasm
G=1-171	C	cytoplasmic mRNA processing body
G=1-171	F	single-stranded DNA binding
G=1-171	F	single-stranded RNA binding
G=1-171	P	positive regulation of translational initiation
G=1-171	P	nuclear-transcribed mRNA catabolic process, exonucleolytic
G=1-171	P	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
I=1-122	F	zinc ion binding
I=1-122	P	transcription initiation from RNA polymerase II promoter
I=1-122	P	maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase II promoter
I=1-122	P	transcription-coupled nucleotide-excision repair
L=1-70	C	DNA-directed RNA polymerase I complex
L=1-70	C	DNA-directed RNA polymerase II, core complex
L=1-70	C	DNA-directed RNA polymerase III complex
L=1-70	F	DNA-directed RNA polymerase activity
L=1-70	F	metal ion binding
L=1-70	F	DNA binding
L=1-70	P	transcription from RNA polymerase I promoter
L=1-70	P	transcription from RNA polymerase II promoter
L=1-70	P	transcription from RNA polymerase III promoter

Sequences

Download file with secondary structure created by Stride

2r92.pdb1.pdb: [ download sequences in FASTA format ]

A (protein):