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


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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	1.3e-14	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):