General information
PDB ID 2R93
Title ELONGATION COMPLEX OF RNA POLYMERASE II WITH A HEPATITIS DELTA VIRUS- DERIVED RNA STEM LOOP
PDB header TRANSFERASE/RNA
Date 2007-09-12
Experimental method X-RAY DIFFRACTION
Resolution (A) 4
Kind rna
Organism SACCHAROMYCES CEREVISIAE
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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:
pdb2r93.pdb ABCDEFGHIJKL R 0
Biounits:
2r93.pdb1.pdb ABCDEFGHIJKL R 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 3.1e-115 1 No_clan A 11 340 R   
RNA_pol_Rpb1_5 Domain P04050_807-1397 1.8e-93 1 No_clan A 807 1397 R   
RNA_pol_Rpb1_2 Domain P04050_342-507 1.9e-77 1 No_clan A 342 507 R   
RNA_pol_Rpb1_6 Domain P04050_873-1056 6.7e-65 1 No_clan A 873 1056   
RNA_pol_Rpb1_3 Domain P04050_510-669 7.5e-47 1 No_clan A 510 669   
RNA_pol_Rpb1_7 Domain P04050_1141-1274 6.6e-39 1 No_clan A 1141 1274   
RNA_pol_Rpb1_4 Domain P04050_693-800 6.4e-35 1 No_clan A 693 800   
RNA_pol_Rpb2_6 Domain P08518_752-1124 7.7e-122 1 CL0410 B 752 1124 R   
RNA_pol_Rpb2_2 Domain P08518_219-407 2.6e-51 1 No_clan B 219 407   
RNA_pol_Rpb2_7 Domain P08518_1126-1219 1.6e-33 1 No_clan B 1126 1219 R   
RNA_pol_Rpb2_4 Domain P08518_580-641 1.9e-25 1 No_clan B 580 641   
RNA_pol_Rpb2_3 Domain P08518_481-545 7.3e-20 1 No_clan B 481 545   
RNA_pol_Rpb2_5 Domain P08518_681-745 2.6e-19 1 No_clan B 681 745   
RNA_pol_A_bac Domain P16370_49-171 8.4e-32 1 No_clan C 49 171   
RNA_pol_L Domain P16370_19-255 3.9e-20 1 CL0509 C 19 255   
RNA_pol_Rpb5_C Domain P20434_142-214 1.4e-30 1 No_clan E 142 214   
RNA_pol_Rpb5_N Domain P20434_6-100 3.3e-29 1 CL0236 E 6 100   
S1 Domain P34087_80-161 5.5e-18 1 CL0021 G 80 161   
SHS2_Rpb7-N Domain P34087_8-66 3.3e-12 1 CL0319 G 8 66   
RNA_POL_M_15KD Domain P27999_4-41 1.3e-17 1 CL0167 I 4 41   
TFIIS_C Domain P27999_73-111 1.2e-14 1 CL0167 I 73 111   
RNA_pol_N Domain P22139_2-60 8.1e-29 1 No_clan J 2 60   
RNA_pol_L_2 Domain P38902_30-104 4.7e-25 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain P40422_29-60 1e-16 1 CL0167 L 29 60   
RNA_pol_Rpb2_1 Family P08518_42-455 9.8e-54 1 No_clan B 42 455   
RNA_pol_Rpb4 Family P20433_49-218 3e-40 1 CL0426 D 49 218   
RNA_pol_Rpb6 Family P20435_79-132 3.1e-14 1 No_clan F 79 132   
RNA_pol_Rpb8 Family P20436_7-146 1.8e-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 R -
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 R -
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:
A=1-1733 C cytoplasmic stress granule
A=1-1733 C mitochondrion
A=1-1733 C nucleus
A=1-1733 C RNA polymerase II, core complex
A=1-1733 F DNA binding
A=1-1733 F DNA-directed 5'-3' RNA polymerase activity
A=1-1733 F metal ion binding
A=1-1733 P transcription by RNA polymerase II
A=1-1733 P transcription, RNA-templated
A=1-1733 P translesion synthesis
B=1-1224 C cytoplasmic stress granule
B=1-1224 C mitochondrion
B=1-1224 C nucleus
B=1-1224 C RNA polymerase II, core complex
B=1-1224 F DNA binding
B=1-1224 F DNA-directed 5'-3' RNA polymerase activity
B=1-1224 F metal ion binding
B=1-1224 F mRNA binding
B=1-1224 F ribonucleoside binding
B=1-1224 P transcription by RNA polymerase II
B=1-1224 P transcription, RNA-templated
C=1-318 C nucleoplasm
C=1-318 C RNA polymerase II, core complex
C=1-318 F DNA binding
C=1-318 F DNA-directed 5'-3' RNA polymerase activity
C=1-318 F metal ion binding
C=1-318 F protein dimerization activity
C=1-318 P termination of RNA polymerase II transcription
C=1-318 P transcription by RNA polymerase II
C=1-318 P transcription, RNA-templated
D=1-221 C cytoplasm
D=1-221 C nucleus
D=1-221 C P-body
D=1-221 C RNA polymerase II, core complex
D=1-221 F DNA-directed 5'-3' RNA polymerase activity
D=1-221 F nucleotide binding
D=1-221 F translation initiation factor binding
D=1-221 P mRNA export from nucleus in response to heat stress
D=1-221 P nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D=1-221 P positive regulation of translational initiation
D=1-221 P recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
D=1-221 P transcription by RNA polymerase II
D=1-221 P transcription initiation from RNA polymerase II promoter
D=1-221 P transcription, RNA-templated
E=1-215 C host cell nucleus
E=1-215 C nucleoplasm
E=1-215 C RNA polymerase I complex
E=1-215 C RNA polymerase II, core complex
E=1-215 C RNA polymerase III complex
E=1-215 F DNA binding
E=1-215 F RNA polymerase I activity
E=1-215 P ribosome biogenesis
E=1-215 P termination of RNA polymerase III transcription
E=1-215 P transcription by RNA polymerase I
E=1-215 P transcription by RNA polymerase II
E=1-215 P transcription by RNA polymerase III
E=1-215 P transcription, RNA-templated
E=1-215 P tRNA transcription by RNA polymerase III
F=1-155 C cytoplasm
F=1-155 C nucleoplasm
F=1-155 C RNA polymerase I complex
F=1-155 C RNA polymerase II, core complex
F=1-155 C RNA polymerase III complex
F=1-155 F DNA binding
F=1-155 F RNA polymerase I activity
F=1-155 P ribosome biogenesis
F=1-155 P termination of RNA polymerase III transcription
F=1-155 P transcription by RNA polymerase I
F=1-155 P transcription by RNA polymerase II
F=1-155 P transcription by RNA polymerase III
F=1-155 P transcription, RNA-templated
F=1-155 P tRNA transcription by RNA polymerase III
G=1-171 C cytoplasm
G=1-171 C nucleus
G=1-171 C P-body
G=1-171 C RNA polymerase II, core complex
G=1-171 F DNA-directed 5'-3' RNA polymerase activity
G=1-171 F single-stranded DNA binding
G=1-171 F single-stranded RNA binding
G=1-171 F translation initiation factor binding
G=1-171 P nuclear-transcribed mRNA catabolic process, exonucleolytic
G=1-171 P positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
G=1-171 P positive regulation of translational initiation
G=1-171 P transcription by RNA polymerase II
G=1-171 P transcription initiation from RNA polymerase II promoter
G=1-171 P transcription, RNA-templated
H=1-146 C nucleoplasm
H=1-146 C RNA polymerase I complex
H=1-146 C RNA polymerase II, core complex
H=1-146 C RNA polymerase III complex
H=1-146 F DNA binding
H=1-146 F RNA polymerase I activity
H=1-146 P ribosome biogenesis
H=1-146 P termination of RNA polymerase III transcription
H=1-146 P transcription by RNA polymerase I
H=1-146 P transcription by RNA polymerase II
H=1-146 P transcription by RNA polymerase III
H=1-146 P transcription, RNA-templated
H=1-146 P tRNA transcription by RNA polymerase III
I=1-122 C nucleolus
I=1-122 C RNA polymerase II, core complex
I=1-122 F DNA-directed 5'-3' RNA polymerase activity
I=1-122 F nucleic acid binding
I=1-122 F zinc ion binding
I=1-122 P maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
I=1-122 P mRNA cleavage
I=1-122 P transcription by RNA polymerase II
I=1-122 P transcription initiation from RNA polymerase II promoter
I=1-122 P transcription, RNA-templated
I=1-122 P transcription-coupled nucleotide-excision repair
J=1-70 C nucleoplasm
J=1-70 C RNA polymerase I complex
J=1-70 C RNA polymerase II, core complex
J=1-70 C RNA polymerase III complex
J=1-70 F DNA binding
J=1-70 F RNA polymerase I activity
J=1-70 F zinc ion binding
J=1-70 P ribosome biogenesis
J=1-70 P termination of RNA polymerase III transcription
J=1-70 P transcription by RNA polymerase I
J=1-70 P transcription by RNA polymerase II
J=1-70 P transcription by RNA polymerase III
J=1-70 P transcription, RNA-templated
J=1-70 P tRNA transcription by RNA polymerase III
K=1-120 C RNA polymerase II, core complex
K=1-120 F DNA binding
K=1-120 F protein dimerization activity
K=1-120 F RNA polymerase II activity
K=1-120 P termination of RNA polymerase II transcription
K=1-120 P transcription by RNA polymerase II
K=1-120 P transcription, RNA-templated
L=1-70 C cytoplasm
L=1-70 C nucleolus
L=1-70 C nucleoplasm
L=1-70 C nucleus
L=1-70 C RNA polymerase I complex
L=1-70 C RNA polymerase II, core complex
L=1-70 C RNA polymerase III complex
L=1-70 F DNA binding
L=1-70 F RNA polymerase I activity
L=1-70 F zinc ion binding
L=1-70 P ribosome biogenesis
L=1-70 P termination of RNA polymerase III transcription
L=1-70 P transcription by RNA polymerase I
L=1-70 P transcription by RNA polymerase II
L=1-70 P transcription by RNA polymerase III
L=1-70 P transcription, RNA-templated
L=1-70 P tRNA transcription by RNA polymerase III
Sequences
Download file with secondary structure created by Stride  
2r93.pdb1.pdb:   [ download sequences in FASTA format ]
A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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K (protein): 
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L (protein): 
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R (rna): 
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