General information
PDB ID 6GMH
Title STRUCTURE OF ACTIVATED TRANSCRIPTION COMPLEX POL II-DSIF-PAF-SPT6
PDB header TRANSCRIPTION
Date 2018-05-26
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.1
Kind hybrid
Organism SUS SCROFA, HOMO SAPIENS, SYNTHETIC CONSTRUCT
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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:
pdb6gmh.pdb ABCDEFGHIJKLMQUVWXYZ NT P 0
Biounits:
6gmh.pdb1.pdb ABCDEFGHIJKLMQUVWXYZ 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_1 Domain I3LJR4_15-354 2.7e-103 1 No_clan A 15 354 PT  H-Bb L-Mj L-Mn 
RNA_pol_Rpb1_5 Domain I3LJR4_811-1399 4.3e-101 1 No_clan A 830 1427 T  H-Mn 
RNA_pol_Rpb1_2 Domain I3LJR4_356-493 2.2e-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 6.4e-38 1 No_clan A 716 823   
RNA_pol_Rpb1_7 Domain I3LJR4_1145-1279 1.5e-37 1 No_clan A 1164 1299   
RNA_pol_Rpb2_6 Domain I3LGP4_784-1157 2.9e-123 1 CL0410 B 707 1080 PTN  L-Bb 
RNA_pol_Rpb2_2 Domain I3LGP4_278-471 3.1e-53 1 No_clan B 201 394   
RNA_pol_Rpb2_7 Domain I3LGP4_1159-1251 6.1e-34 1 No_clan B 1082 1174 T   
RNA_pol_Rpb2_4 Domain I3LGP4_644-706 2.7e-24 1 No_clan B 567 629   
RNA_pol_Rpb2_3 Domain I3LGP4_545-609 1e-23 1 No_clan B 468 532 P   
RNA_pol_Rpb2_5 Domain I3LGP4_730-777 2.2e-16 1 No_clan B 653 700   
RNA_pol_A_bac Domain I3LCH3_50-177 3.1e-40 1 No_clan C 50 177   
RNA_pol_L Domain I3LCH3_20-256 3e-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 N  H-Bb L-Bb 
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   
YqgF Domain Q7KZ85_775-931 6e-70 1 CL0580 M 775 931 P   
SH2_2 Domain Q7KZ85_1327-1514 1.1e-56 1 CL0541 M 1332 1514   
HHH_7 Domain Q7KZ85_935-1038 1.2e-52 1 CL0198 M 935 1038   
HTH_44 Domain Q7KZ85_305-430 6.9e-27 1 No_clan M 305 427   
S1 Domain Q7KZ85_1226-1282 5.6e-08 1 CL0021 M 1163 1282   
Tex_N Domain Q7KZ85_56-245 1.1e-05 0 No_clan M 354 619   
HHH_9 Domain Q7KZ85_1051-1138 2.1e-05 1 CL0198 M 1051 1138   
TPR_19 Domain Q6PD62_992-1055 7.9e-05 0 CL0020 Q 691 754   
TPR_19 Domain Q6PD62_927-991 0.00051 0 CL0020 Q 626 690   
Spt4 Domain P63272_13-90 8.7e-33 1 CL0167 Y 13 90   
RNA_pol_Rpb2_1 Family I3LGP4_115-519 1.4e-67 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   
Spt5-NGN Family O00267_178-264 4.6e-27 1 CL0439 Z 178 264   
KOW Family O00267_474-505 5.4e-08 1 CL0107 Z 474 505   
KOW Family O00267_474-505 4.8e-05 1 CL0107 Z 706 737   
KOW Family O00267_474-505 0.00085 0 CL0107 Z 596 627   
TPR_12 Repeat Q6PD62_796-864 1.1e-06 0 CL0020 Q 495 563   
TPR_2 Repeat Q6PD62_643-675 7.7e-05 0 CL0020 Q 342 374   
WD40 Repeat Q9GZS3_54-92 2e-09 1 CL0186 W 180 218   
WD40 Repeat Q9GZS3_54-92 4e-07 1 CL0186 W 222 260   
eIF2A Repeat Q9GZS3_7-131 0.00082 0 CL0186 W 10 134   
WD40 Repeat Q9GZS3_54-92 0.00087 1 CL0186 W 138 176   
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
M=1-1726 C nucleoplasm
M=1-1726 C transcription elongation factor complex
M=1-1726 C transcriptionally active chromatin
M=1-1726 F DNA binding
M=1-1726 F histone binding
M=1-1726 F nucleosome binding
M=1-1726 F RNA binding
M=1-1726 P blastocyst formation
M=1-1726 P chromatin maintenance
M=1-1726 P mRNA processing
M=1-1726 P mRNA transcription by RNA polymerase II
M=1-1726 P mRNA transport
M=1-1726 P negative regulation of histone H3-K27 methylation
M=1-1726 P nucleosome organization
M=1-1726 P positive regulation of transcription elongation from RNA polymerase II promoter
M=1-1726 P regulation of isotype switching
M=1-1726 P regulation of mRNA export from nucleus
M=1-1726 P regulation of mRNA processing
M=1-1726 P regulation of muscle cell differentiation
M=1-1726 P RNA splicing
M=1-1726 P transcription by RNA polymerase II
M=1-1726 P transcription elongation from RNA polymerase II promoter
M=1-1726 P viral process
Q=301-1173 C Cdc73/Paf1 complex
Q=301-1173 C nuclear speck
Q=301-1173 C nucleoplasm
Q=301-1173 C transcriptionally active chromatin
Q=301-1173 F RNA polymerase II complex binding
Q=301-1173 F SH2 domain binding
Q=301-1173 P blastocyst growth
Q=301-1173 P blastocyst hatching
Q=301-1173 P cellular response to lipopolysaccharide
Q=301-1173 P endodermal cell fate commitment
Q=301-1173 P histone H2B ubiquitination
Q=301-1173 P histone H3-K4 trimethylation
Q=301-1173 P histone monoubiquitination
Q=301-1173 P inner cell mass cell differentiation
Q=301-1173 P interleukin-6-mediated signaling pathway
Q=301-1173 P negative regulation of mRNA polyadenylation
Q=301-1173 P negative regulation of myeloid cell differentiation
Q=301-1173 P negative regulation of transcription by RNA polymerase II
Q=301-1173 P positive regulation of histone H2B ubiquitination
Q=301-1173 P positive regulation of histone H3-K4 methylation
Q=301-1173 P positive regulation of histone H3-K79 methylation
Q=301-1173 P protein ubiquitination
Q=301-1173 P receptor signaling pathway via JAK-STAT
Q=301-1173 P regulation of genetic imprinting
Q=301-1173 P regulation of histone H3-K4 methylation
Q=301-1173 P regulation of transcription, DNA-templated
Q=301-1173 P stem cell population maintenance
Q=301-1173 P transcription by RNA polymerase II
Q=301-1173 P transcription elongation from RNA polymerase II promoter
Q=301-1173 P trophectodermal cell differentiation
Q=301-1173 P Wnt signaling pathway
U=1-666 C Cdc73/Paf1 complex
U=1-666 C centrosome
U=1-666 C fibrillar center
U=1-666 C nucleoplasm
U=1-666 C nucleus
U=1-666 F RNA polymerase II C-terminal domain phosphoserine binding
U=1-666 P beta-catenin-TCF complex assembly
U=1-666 P endodermal cell fate commitment
U=1-666 P histone H2B ubiquitination
U=1-666 P histone monoubiquitination
U=1-666 P mRNA polyadenylation
U=1-666 P negative regulation of myeloid cell differentiation
U=1-666 P positive regulation of mRNA 3'-end processing
U=1-666 P positive regulation of transcription elongation from RNA polymerase II promoter
U=1-666 P protein ubiquitination
U=1-666 P stem cell population maintenance
U=1-666 P transcription by RNA polymerase II
U=1-666 P transcription elongation from RNA polymerase II promoter
U=1-666 P Wnt signaling pathway
V=1-531 C Cdc73/Paf1 complex
V=1-531 C cell junction
V=1-531 C cytoplasm
V=1-531 C membrane
V=1-531 C nucleoplasm
V=1-531 C transcriptionally active chromatin
V=1-531 F chromatin binding
V=1-531 F RNA polymerase II complex binding
V=1-531 P cellular response to lipopolysaccharide
V=1-531 P endodermal cell fate commitment
V=1-531 P histone H2B ubiquitination
V=1-531 P histone monoubiquitination
V=1-531 P mRNA polyadenylation
V=1-531 P negative regulation of myeloid cell differentiation
V=1-531 P negative regulation of transcription by RNA polymerase II
V=1-531 P nucleosome positioning
V=1-531 P positive regulation of cell cycle G1/S phase transition
V=1-531 P positive regulation of histone methylation
V=1-531 P positive regulation of mRNA 3'-end processing
V=1-531 P protein localization to nucleus
V=1-531 P protein ubiquitination
V=1-531 P stem cell population maintenance
V=1-531 P transcription by RNA polymerase II
V=1-531 P transcription elongation from RNA polymerase II promoter
V=1-531 P Wnt signaling pathway
W=1-305 C Cdc73/Paf1 complex
W=1-305 C cytoplasm
W=1-305 C cytosol
W=1-305 C nucleoplasm
W=1-305 C nucleus
W=1-305 C Ski complex
W=1-305 C transcriptionally active chromatin
W=1-305 P exonucleolytic catabolism of deadenylated mRNA
W=1-305 P histone H3-K4 trimethylation
W=1-305 P negative regulation of myeloid cell differentiation
W=1-305 P positive regulation of histone H3-K4 methylation
W=1-305 P positive regulation of histone H3-K79 methylation
W=1-305 P protein ubiquitination
W=1-305 P transcription by RNA polymerase II
W=1-305 P transcription elongation from RNA polymerase II promoter
W=1-305 P Wnt signaling pathway
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  
6gmh.pdb1.pdb:   [ download sequences in FASTA format ]
N (dna): 
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T (dna): 
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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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M (protein): 
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Q (protein): 
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U (protein): 
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V (protein): 
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W (protein): 
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X (protein): 
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Y (protein): 
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Z (protein): 
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P (rna): 
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