General information
PDB ID 6J51
Title RNA POLYMERASE II ELONGATION COMPLEX BOUND WITH SPT4/5 AND FOREIGN DNA, STALLED AT SHL(-1) OF THE NUCLEOSOME, WEAK ELF1 (+1 POSITION)
PDB header TRANSCRIPTION/RNA/DNA
Date 2019-01-10
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.2
Kind hybrid
Organism SYNTHETIC CONSTRUCT, HOMO SAPIENS
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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:
pdb6j51.pdb ABCDEFGHIJKLMVWabcdefgh TN01 P 0
Biounits:
6j51.pdb1.pdb ABCDEFGHIJKLMVWabcdefgh TN01 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 C4R4Y0_11-341 9.2e-115 1 No_clan A 11 341 NTP   
RNA_pol_Rpb1_5 Domain C4R4Y0_808-1400 3.1e-90 1 No_clan A 808 1400 T   
RNA_pol_Rpb1_2 Domain C4R4Y0_343-508 2.7e-77 1 No_clan A 343 508 PT   
RNA_pol_Rpb1_6 Domain C4R4Y0_874-1058 2.1e-66 1 No_clan A 874 1058   
RNA_pol_Rpb1_3 Domain C4R4Y0_511-670 1.7e-46 1 No_clan A 511 670   
Histone Domain P84243_39-132 1.4e-45 1 CL0012 a 38 131 NT   
RNA_pol_Rpb1_7 Domain C4R4Y0_1143-1277 5.8e-37 1 No_clan A 1143 1277   
RNA_pol_Rpb1_4 Domain C4R4Y0_694-801 4e-34 1 No_clan A 694 801   
RNA_pol_Rpb2_6 Domain C4QZQ7_752-1124 3.6e-121 1 CL0410 B 752 1124 PT   
RNA_pol_Rpb2_2 Domain C4QZQ7_210-400 1.3e-49 1 No_clan B 210 400   
RNA_pol_Rpb2_7 Domain C4QZQ7_1126-1219 6.5e-34 1 No_clan B 1126 1219 T   
RNA_pol_Rpb2_4 Domain C4QZQ7_573-634 4.2e-24 1 No_clan B 573 634   
RNA_pol_Rpb2_3 Domain C4QZQ7_474-538 6.1e-24 1 No_clan B 474 538 N   
RNA_pol_Rpb2_5 Domain C4QZQ7_678-745 6e-20 1 No_clan B 678 745   
CENP-T_C Domain P62805_26-99 4.6e-08 1 CL0012 b 26 98 NT   
RNA_pol_A_bac Domain C4R7L2_48-171 3.3e-32 1 No_clan C 48 171 N   
RNA_pol_L Domain C4R7L2_18-255 1.5e-19 1 CL0509 C 18 255 NT   
Histone Domain P04908_16-91 5.7e-16 1 CL0012 c 16 90 NT   
Histone Domain P06899_33-102 5.7e-22 1 CL0012 d 28 98 NT   
Histone Domain P84243_39-132 3.4e-45 1 CL0012 e 39 131 NT   
RNA_pol_Rpb5_C Domain C4R3P8_141-213 1.2e-31 1 No_clan E 141 213   
RNA_pol_Rpb5_N Domain C4R3P8_5-99 8.7e-28 1 CL0236 E 5 99 NT   
CENP-T_C Domain P62805_26-99 4.2e-08 1 CL0012 f 26 98 NT   
Histone Domain P04908_16-91 4.3e-16 1 CL0012 g 14 90 01   
S1 Domain C4R9A1_80-164 6.4e-13 1 CL0021 G 80 164   
SHS2_Rpb7-N Domain C4R9A1_8-66 1.4e-12 1 CL0319 G 8 66 01   
Histone Domain P06899_33-102 2.6e-21 1 CL0012 h 31 98 01   
TFIIS_C Domain F2QPE6_73-111 2.1e-15 1 CL0167 I 73 111   
RNA_POL_M_15KD Domain F2QPE6_4-41 1.1e-13 1 CL0167 I 4 41   
RNA_pol_N Domain C4R009_2-59 1.7e-31 1 No_clan J 2 59   
RNA_pol_L_2 Domain C4R3Z5_30-104 2.4e-23 1 CL0509 K 30 104   
DNA_RNApol_7kD Domain F2QMI1_31-62 3.2e-17 1 CL0167 L 31 62   
Elf1 Domain C4QZ45_15-78 6.9e-26 1 CL0167 M 15 78   
Spt4 Domain C4R0E6_9-87 6.3e-30 1 CL0167 V 9 87   
RNA_pol_Rpb2_1 Family C4QZQ7_29-448 4.8e-67 1 No_clan B 29 448 NT   
Histone_H2A_C Family P04908_92-119 2.3e-17 1 No_clan c 91 118   
RNA_pol_Rpb4 Family C4R2U9_50-182 7.5e-21 1 CL0426 D 50 182 T   
RNA_pol_Rpb6 Family C4R1V1_79-132 6.9e-14 1 No_clan F 79 132   
Histone_H2A_C Family P04908_92-119 2.4e-17 1 No_clan g 91 118   
RNA_pol_Rpb8 Family C4R273_7-145 1.4e-42 1 CL0021 H 7 145 01   
Spt5-NGN Family C4R370_225-310 9.2e-21 1 CL0439 W 225 310 N   
KOW Family 4.4e-05 1 CL0107 W 753 783
KOW Family 0.00085 0 CL0107 W 322 353
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
a/e=1-136 C Barr body
a/e=1-136 C extracellular exosome
a/e=1-136 C extracellular region
a/e=1-136 C nuclear chromosome
a/e=1-136 C nuclear chromosome, telomeric region
a/e=1-136 C nuclear nucleosome
a/e=1-136 C nucleoplasm
a/e=1-136 C nucleosome
a/e=1-136 C nucleus
a/e=1-136 C protein-containing complex
a/e=1-136 F nucleosomal DNA binding
a/e=1-136 F protein heterodimerization activity
a/e=1-136 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
a/e=1-136 F RNA polymerase II core promoter sequence-specific DNA binding
a/e=1-136 P blood coagulation
a/e=1-136 P brain development
a/e=1-136 P cell population proliferation
a/e=1-136 P cellular protein metabolic process
a/e=1-136 P DNA replication-independent nucleosome assembly
a/e=1-136 P embryo implantation
a/e=1-136 P male gonad development
a/e=1-136 P multicellular organism growth
a/e=1-136 P muscle cell differentiation
a/e=1-136 P negative regulation of chromosome condensation
a/e=1-136 P negative regulation of gene expression, epigenetic
a/e=1-136 P nucleosome assembly
a/e=1-136 P nucleus organization
a/e=1-136 P oogenesis
a/e=1-136 P osteoblast differentiation
a/e=1-136 P pericentric heterochromatin assembly
a/e=1-136 P positive regulation of cell growth
a/e=1-136 P rDNA heterochromatin assembly
a/e=1-136 P regulation of centromere complex assembly
a/e=1-136 P regulation of gene silencing by miRNA
a/e=1-136 P regulation of megakaryocyte differentiation
a/e=1-136 P response to hormone
a/e=1-136 P single fertilization
a/e=1-136 P spermatid development
a/e=1-136 P subtelomeric heterochromatin assembly
a/e=1-136 P telomere organization
b/f=1-103 C extracellular exosome
b/f=1-103 C extracellular region
b/f=1-103 C host cell nucleus
b/f=1-103 C membrane
b/f=1-103 C nuclear chromosome
b/f=1-103 C nuclear chromosome, telomeric region
b/f=1-103 C nuclear nucleosome
b/f=1-103 C nucleoplasm
b/f=1-103 C nucleosome
b/f=1-103 C nucleus
b/f=1-103 C protein-containing complex
b/f=1-103 F DNA binding
b/f=1-103 F protein domain specific binding
b/f=1-103 F protein heterodimerization activity
b/f=1-103 F RNA binding
b/f=1-103 P cellular protein metabolic process
b/f=1-103 P CENP-A containing nucleosome assembly
b/f=1-103 P DNA replication-dependent nucleosome assembly
b/f=1-103 P DNA replication-independent nucleosome assembly
b/f=1-103 P DNA-templated transcription, initiation
b/f=1-103 P double-strand break repair via nonhomologous end joining
b/f=1-103 P negative regulation of gene expression, epigenetic
b/f=1-103 P negative regulation of megakaryocyte differentiation
b/f=1-103 P nucleosome assembly
b/f=1-103 P rDNA heterochromatin assembly
b/f=1-103 P regulation of gene silencing by miRNA
b/f=1-103 P regulation of megakaryocyte differentiation
b/f=1-103 P telomere capping
b/f=1-103 P telomere organization
c/g=1-130 C extracellular exosome
c/g=1-130 C nuclear chromatin
c/g=1-130 C nucleosome
c/g=1-130 C nucleus
c/g=1-130 F DNA binding
c/g=1-130 F protein heterodimerization activity
c/g=1-130 P chromatin organization
c/g=1-130 P chromatin silencing
c/g=1-130 P negative regulation of cell population proliferation
d/h=1-126 C cytosol
d/h=1-126 C extracellular space
d/h=1-126 C nucleoplasm
d/h=1-126 C nucleosome
d/h=1-126 C nucleus
d/h=1-126 F DNA binding
d/h=1-126 F lipopolysaccharide binding
d/h=1-126 F protein heterodimerization activity
d/h=1-126 P antibacterial humoral response
d/h=1-126 P antimicrobial humoral immune response mediated by antimicrobial peptide
d/h=1-126 P defense response to Gram-negative bacterium
d/h=1-126 P defense response to Gram-positive bacterium
d/h=1-126 P innate immune response in mucosa
d/h=1-126 P killing of cells of other organism
d/h=1-126 P negative regulation of tumor necrosis factor-mediated signaling pathway
d/h=1-126 P nucleosome assembly
d/h=1-126 P protein ubiquitination
Sequences
Download file with secondary structure created by Stride  
6j51.pdb1.pdb:   [ download sequences in FASTA format ]
0 (dna): 
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1 (dna): 
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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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V (protein): 
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W (protein): 
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P (rna): 
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