General information
PDB ID 6GML
Title STRUCTURE OF PAUSED TRANSCRIPTION COMPLEX POL II-DSIF-NELF
PDB header TRANSCRIPTION
Date 2018-05-27
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.2
Kind hybrid
Organism SUS SCROFA, HUMAN IMMUNODEFICIENCY VIRUS 1, HOMO SAPIENS
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:
pdb6gml.pdb ABCEFHIJKLUVWXYZDG NT P 0
Biounits:
6gml.pdb1.pdb ABCEFHIJKLUVWXYZDG NT P 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RNA_pol_Rpb1_5 Domain I3LJR4_811-1399 4.1e-101 1 No_clan A 830 1427 NT  L-Bb 
RNA_pol_Rpb1_1 Domain I3LJR4_15-354 9.6e-101 1 No_clan A 15 354 TP  H-Bb L-Bb 
RNA_pol_Rpb1_2 Domain I3LJR4_356-493 2.1e-74 1 No_clan A 356 521 PT   
RNA_pol_Rpb1_6 Domain I3LJR4_877-1060 1.6e-68 1 No_clan A 896 1079   
RNA_pol_Rpb1_3 Domain I3LJR4_508-673 1.2e-49 1 No_clan A 524 692   
RNA_pol_Rpb1_4 Domain I3LJR4_697-804 6.2e-38 1 No_clan A 716 823   
RNA_pol_Rpb1_7 Domain I3LJR4_1145-1279 1.7e-37 1 No_clan A 1164 1299   
RNA_pol_Rpb2_6 Domain I3LGP4_784-1157 1.8e-126 1 CL0410 B 707 1080 PT   
RNA_pol_Rpb2_2 Domain I3LGP4_278-471 1.7e-53 1 No_clan B 201 394   
RNA_pol_Rpb2_7 Domain I3LGP4_1159-1251 6e-34 1 No_clan B 1082 1174 T   
RNA_pol_Rpb2_4 Domain I3LGP4_644-706 2.6e-24 1 No_clan B 567 629   
RNA_pol_Rpb2_3 Domain I3LGP4_545-609 1e-23 1 No_clan B 468 532 NP  L-Bb 
RNA_pol_Rpb2_5 Domain I3LGP4_730-777 2.1e-16 1 No_clan B 653 700   
RNA_pol_A_bac Domain I3LCH3_50-177 1.8e-40 1 No_clan C 50 177   
RNA_pol_L Domain I3LCH3_20-256 2.8e-17 1 CL0509 C 20 256   
RNA_pol_Rpb5_C Domain I3LSI7_137-209 2.8e-34 1 No_clan E 137 209   
RNA_pol_Rpb5_N Domain I3LSI7_4-94 1.3e-33 1 CL0236 E 4 94   
S1 Domain I3LJZ9_78-161 1e-20 1 CL0021 G 78 161   
SHS2_Rpb7-N Domain I3LJZ9_8-64 2.7e-10 1 CL0319 G 8 64   
RNA_POL_M_15KD Domain P60899_14-51 3.9e-17 1 CL0167 I 14 51   
TFIIS_C Domain P60899_84-124 8.1e-12 1 CL0167 I 84 124   
RNA_pol_N Domain 3.6e-32 1 No_clan J 2 59
RNA_pol_L_2 Domain F1RKE4_30-104 3.2e-29 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain I3LN51_17-48 8.3e-18 1 CL0167 L 17 48   
Spt4 Domain P63272_13-90 8.7e-33 1 CL0167 Y 13 90   
RNA_pol_Rpb2_1 Family I3LGP4_115-519 8.5e-62 1 No_clan B 38 442   
RNA_pol_Rpb4 Family A0A287ADR4_73-180 1.1e-25 1 CL0426 D 31 138   
RNA_pol_Rpb6 Family F1SKN8_51-104 2.1e-13 1 No_clan F 51 104   
RNA_pol_Rpb8 Family I3LCB2_7-147 5.6e-54 1 CL0021 H 7 147   
COBRA1 Family Q8WX92_212-392 5.7e-98 1 No_clan V 177 410   
COBRA1 Family Q8WX92_142-215 1.9e-36 1 No_clan V 103 201   
COBRA1 Family Q8WX92_389-427 0.001 0 No_clan V 388 450   
TH1 Family Q8IXH7_51-587 2.4e-246 1 No_clan W 86 587   
Spt5-NGN Family O00267_178-264 4.4e-27 1 CL0439 Z 178 264   
KOW Family O00267_474-505 5.2e-08 1 CL0107 Z 474 505   
KOW Family O00267_474-505 4.6e-05 1 CL0107 Z 706 737   
KOW Family O00267_474-505 0.00081 0 CL0107 Z 596 627   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
I=1-125 C nucleolus
I=1-125 C nucleus
I=1-125 C RNA polymerase II, core complex
I=1-125 F DNA-directed 5'-3' RNA polymerase activity
I=1-125 F nucleic acid binding
I=1-125 F zinc ion binding
I=1-125 P maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
I=1-125 P mRNA cleavage
I=1-125 P transcription by RNA polymerase II
I=1-125 P transcription initiation from RNA polymerase II promoter
I=1-125 P transcription-coupled nucleotide-excision repair
U=1-528 C cytosol
U=1-528 C NELF complex
U=1-528 C nuclear body
U=1-528 C nucleoplasm
U=1-528 P multicellular organism development
U=1-528 P negative regulation of transcription elongation from RNA polymerase II promoter
U=1-528 P positive regulation of viral transcription
U=1-528 P transcription by RNA polymerase II
U=1-528 P transcription elongation from RNA polymerase II promoter
V=42-580 C cytoplasm
V=42-580 C NELF complex
V=42-580 C nucleoplasm
V=42-580 F RNA binding
V=42-580 P cell population proliferation
V=42-580 P negative regulation of stem cell differentiation
V=42-580 P negative regulation of transcription elongation from RNA polymerase II promoter
V=42-580 P positive regulation of viral transcription
V=42-580 P stem cell differentiation
V=42-580 P transcription by RNA polymerase II
V=42-580 P transcription elongation from RNA polymerase II promoter
W=10-590 C membrane
W=10-590 C NELF complex
W=10-590 C nucleoplasm
W=10-590 F RNA binding
W=10-590 P negative regulation of transcription elongation from RNA polymerase II promoter
W=10-590 P positive regulation of viral transcription
W=10-590 P transcription by RNA polymerase II
W=10-590 P transcription elongation from RNA polymerase II promoter
X=1-380 C NELF complex
X=1-380 C nuclear body
X=1-380 C nucleoplasm
X=1-380 C nucleus
X=1-380 C plasma membrane
X=1-380 F chromatin binding
X=1-380 F RNA binding
X=1-380 P negative regulation of mRNA polyadenylation
X=1-380 P negative regulation of transcription elongation from RNA polymerase II promoter
X=1-380 P positive regulation of ERK1 and ERK2 cascade
X=1-380 P positive regulation of histone H3-K4 methylation
X=1-380 P positive regulation of transcription by RNA polymerase II
X=1-380 P positive regulation of viral transcription
X=1-380 P transcription by RNA polymerase II
X=1-380 P transcription elongation from RNA polymerase II promoter
Y=1-117 C DSIF complex
Y=1-117 C nucleoplasm
Y=1-117 F protein heterodimerization activity
Y=1-117 F RNA polymerase II complex binding
Y=1-117 F single-stranded RNA binding
Y=1-117 F zinc ion binding
Y=1-117 P chromatin organization
Y=1-117 P mRNA processing
Y=1-117 P negative regulation of DNA-templated transcription, elongation
Y=1-117 P negative regulation of transcription by RNA polymerase II
Y=1-117 P negative regulation of transcription elongation from RNA polymerase II promoter
Y=1-117 P positive regulation of DNA-templated transcription, elongation
Y=1-117 P positive regulation of transcription by RNA polymerase II
Y=1-117 P positive regulation of viral transcription
Y=1-117 P regulation of transcription elongation from RNA polymerase II promoter
Y=1-117 P regulation of transcription, DNA-templated
Y=1-117 P transcription by RNA polymerase II
Y=1-117 P transcription elongation from RNA polymerase II promoter
Z=1-1087 C DSIF complex
Z=1-1087 C nucleoplasm
Z=1-1087 C nucleus
Z=1-1087 F chromatin binding
Z=1-1087 F enzyme binding
Z=1-1087 F mRNA binding
Z=1-1087 F protein heterodimerization activity
Z=1-1087 F RNA binding
Z=1-1087 P 7-methylguanosine mRNA capping
Z=1-1087 P negative regulation of DNA-templated transcription, elongation
Z=1-1087 P negative regulation of mRNA polyadenylation
Z=1-1087 P negative regulation of transcription by RNA polymerase II
Z=1-1087 P positive regulation of DNA-templated transcription, elongation
Z=1-1087 P positive regulation of macroautophagy
Z=1-1087 P positive regulation of transcription by RNA polymerase II
Z=1-1087 P positive regulation of viral transcription
Z=1-1087 P regulation of transcription by RNA polymerase II
Z=1-1087 P transcription by RNA polymerase II
Z=1-1087 P transcription elongation from RNA polymerase II promoter
Sequences
Download file with secondary structure created by Stride  
6gml.pdb1.pdb:   [ download sequences in FASTA format ]
N (dna): 
Click "SHOW" for view sequence
T (dna): 
Click "SHOW" for view sequence
A (protein): 
Click "SHOW" for view sequence
B (protein): 
Click "SHOW" for view sequence
C (protein): 
Click "SHOW" for view sequence
D (protein): 
Click "SHOW" for view sequence
E (protein): 
Click "SHOW" for view sequence
F (protein): 
Click "SHOW" for view sequence
G (protein): 
Click "SHOW" for view sequence
H (protein): 
Click "SHOW" for view sequence
I (protein): 
Click "SHOW" for view sequence
J (protein): 
Click "SHOW" for view sequence
K (protein): 
Click "SHOW" for view sequence
L (protein): 
Click "SHOW" for view sequence
U (protein): 
Click "SHOW" for view sequence
V (protein): 
Click "SHOW" for view sequence
W (protein): 
Click "SHOW" for view sequence
X (protein): 
Click "SHOW" for view sequence
Y (protein): 
Click "SHOW" for view sequence
Z (protein): 
Click "SHOW" for view sequence
P (rna): 
Click "SHOW" for view sequence
© NPIDB team 2003 - 2021

text