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8S5N

RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt

Functional Information from GO Data
ChainGOidnamespacecontents
A0000428cellular_componentDNA-directed RNA polymerase complex
A0003677molecular_functionDNA binding
A0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
A0005634cellular_componentnucleus
A0006351biological_processDNA-templated transcription
A0006366biological_processtranscription by RNA polymerase II
A0016779molecular_functionnucleotidyltransferase activity
A0031981cellular_componentnuclear lumen
A0032991cellular_componentprotein-containing complex
A0046872molecular_functionmetal ion binding
B0000428cellular_componentDNA-directed RNA polymerase complex
B0000781cellular_componentchromosome, telomeric region
B0001055molecular_functionRNA polymerase II activity
B0001172biological_processRNA-templated transcription
B0003677molecular_functionDNA binding
B0003682molecular_functionchromatin binding
B0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
B0003968molecular_functionRNA-dependent RNA polymerase activity
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005665cellular_componentRNA polymerase II, core complex
B0006351biological_processDNA-templated transcription
B0006366biological_processtranscription by RNA polymerase II
B0016779molecular_functionnucleotidyltransferase activity
B0032549molecular_functionribonucleoside binding
B0034062molecular_function5'-3' RNA polymerase activity
B0046872molecular_functionmetal ion binding
C0000428cellular_componentDNA-directed RNA polymerase complex
C0003677molecular_functionDNA binding
C0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005665cellular_componentRNA polymerase II, core complex
C0005829cellular_componentcytosol
C0006351biological_processDNA-templated transcription
C0006366biological_processtranscription by RNA polymerase II
C0046983molecular_functionprotein dimerization activity
D0000166molecular_functionnucleotide binding
D0000428cellular_componentDNA-directed RNA polymerase complex
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005665cellular_componentRNA polymerase II, core complex
D0005829cellular_componentcytosol
D0006352biological_processDNA-templated transcription initiation
D0006366biological_processtranscription by RNA polymerase II
D0006367biological_processtranscription initiation at RNA polymerase II promoter
D0016607cellular_componentnuclear speck
D0030880cellular_componentRNA polymerase complex
D0031369molecular_functiontranslation initiation factor binding
D0044237biological_processcellular metabolic process
E0001054molecular_functionRNA polymerase I activity
E0001055molecular_functionRNA polymerase II activity
E0001056molecular_functionRNA polymerase III activity
E0003677molecular_functionDNA binding
E0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005665cellular_componentRNA polymerase II, core complex
E0005666cellular_componentRNA polymerase III complex
E0005736cellular_componentRNA polymerase I complex
E0006351biological_processDNA-templated transcription
E0006362biological_processtranscription elongation by RNA polymerase I
E0006366biological_processtranscription by RNA polymerase II
E0042797biological_processtRNA transcription by RNA polymerase III
F0000428cellular_componentDNA-directed RNA polymerase complex
F0001650cellular_componentfibrillar center
F0003677molecular_functionDNA binding
F0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005665cellular_componentRNA polymerase II, core complex
F0005666cellular_componentRNA polymerase III complex
F0005736cellular_componentRNA polymerase I complex
F0006351biological_processDNA-templated transcription
F0006366biological_processtranscription by RNA polymerase II
G0000428cellular_componentDNA-directed RNA polymerase complex
G0003676molecular_functionnucleic acid binding
G0005634cellular_componentnucleus
G0006351biological_processDNA-templated transcription
G0006352biological_processDNA-templated transcription initiation
H0000428cellular_componentDNA-directed RNA polymerase complex
H0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
H0005634cellular_componentnucleus
H0005665cellular_componentRNA polymerase II, core complex
H0006351biological_processDNA-templated transcription
I0000428cellular_componentDNA-directed RNA polymerase complex
I0001193biological_processmaintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
I0003676molecular_functionnucleic acid binding
I0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
I0005634cellular_componentnucleus
I0005654cellular_componentnucleoplasm
I0005665cellular_componentRNA polymerase II, core complex
I0005730cellular_componentnucleolus
I0006283biological_processtranscription-coupled nucleotide-excision repair
I0006351biological_processDNA-templated transcription
I0006366biological_processtranscription by RNA polymerase II
I0006367biological_processtranscription initiation at RNA polymerase II promoter
I0008270molecular_functionzinc ion binding
I0046872molecular_functionmetal ion binding
J0000428cellular_componentDNA-directed RNA polymerase complex
J0003677molecular_functionDNA binding
J0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
J0006351biological_processDNA-templated transcription
J0008270molecular_functionzinc ion binding
J0046872molecular_functionmetal ion binding
K0000428cellular_componentDNA-directed RNA polymerase complex
K0001055molecular_functionRNA polymerase II activity
K0003677molecular_functionDNA binding
K0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
K0005634cellular_componentnucleus
K0005665cellular_componentRNA polymerase II, core complex
K0006351biological_processDNA-templated transcription
K0006366biological_processtranscription by RNA polymerase II
K0046983molecular_functionprotein dimerization activity
L0003677molecular_functionDNA binding
L0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
L0005634cellular_componentnucleus
L0005665cellular_componentRNA polymerase II, core complex
L0005666cellular_componentRNA polymerase III complex
L0005736cellular_componentRNA polymerase I complex
L0006351biological_processDNA-templated transcription
L0006366biological_processtranscription by RNA polymerase II
L0008270molecular_functionzinc ion binding
L0046872molecular_functionmetal ion binding
M0000776cellular_componentkinetochore
M0000793cellular_componentcondensed chromosome
M0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
M0000993molecular_functionRNA polymerase II complex binding
M0001174biological_processtranscriptional start site selection at RNA polymerase II promoter
M0003677molecular_functionDNA binding
M0004402molecular_functionhistone acetyltransferase activity
M0005515molecular_functionprotein binding
M0005634cellular_componentnucleus
M0005654cellular_componentnucleoplasm
M0005669cellular_componenttranscription factor TFIID complex
M0005694cellular_componentchromosome
M0006338biological_processchromatin remodeling
M0006352biological_processDNA-templated transcription initiation
M0006366biological_processtranscription by RNA polymerase II
M0006367biological_processtranscription initiation at RNA polymerase II promoter
M0006473biological_processprotein acetylation
M0008270molecular_functionzinc ion binding
M0010467biological_processgene expression
M0016251molecular_functionRNA polymerase II general transcription initiation factor activity
M0016407molecular_functionacetyltransferase activity
M0016604cellular_componentnuclear body
M0016746molecular_functionacyltransferase activity
M0017025molecular_functionTBP-class protein binding
M0019083biological_processviral transcription
M0032153cellular_componentcell division site
M0032993cellular_componentprotein-DNA complex
M0042585cellular_componentgerminal vesicle
M0046872molecular_functionmetal ion binding
M0046966molecular_functionnuclear thyroid hormone receptor binding
M0051123biological_processRNA polymerase II preinitiation complex assembly
M0051177biological_processmeiotic sister chromatid cohesion
M0051225biological_processspindle assembly
M0051276biological_processchromosome organization
M0061733molecular_functionpeptide-lysine-N-acetyltransferase activity
M0070897biological_processtranscription preinitiation complex assembly
M0090575cellular_componentRNA polymerase II transcription regulator complex
M0097550cellular_componenttranscription preinitiation complex
M0140297molecular_functionDNA-binding transcription factor binding
M1904798biological_processpositive regulation of core promoter binding
M1990114biological_processRNA polymerase II core complex assembly
M1990841molecular_functionpromoter-specific chromatin binding
O0000785cellular_componentchromatin
O0000791cellular_componenteuchromatin
O0000976molecular_functiontranscription cis-regulatory region binding
O0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
O0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
O0000995molecular_functionRNA polymerase III general transcription initiation factor activity
O0001046molecular_functioncore promoter sequence-specific DNA binding
O0001091molecular_functionRNA polymerase II general transcription initiation factor binding
O0001093molecular_functionTFIIB-class transcription factor binding
O0001164molecular_functionRNA polymerase I core promoter sequence-specific DNA binding
O0001188biological_processRNA polymerase I preinitiation complex assembly
O0001673cellular_componentmale germ cell nucleus
O0001674cellular_componentfemale germ cell nucleus
O0001939cellular_componentfemale pronucleus
O0001940cellular_componentmale pronucleus
O0003677molecular_functionDNA binding
O0005515molecular_functionprotein binding
O0005634cellular_componentnucleus
O0005654cellular_componentnucleoplasm
O0005668cellular_componentRNA polymerase transcription factor SL1 complex
O0005669cellular_componenttranscription factor TFIID complex
O0005672cellular_componenttranscription factor TFIIA complex
O0005737cellular_componentcytoplasm
O0006352biological_processDNA-templated transcription initiation
O0006366biological_processtranscription by RNA polymerase II
O0006367biological_processtranscription initiation at RNA polymerase II promoter
O0006383biological_processtranscription by RNA polymerase III
O0007283biological_processspermatogenesis
O0016251molecular_functionRNA polymerase II general transcription initiation factor activity
O0017162molecular_functionaryl hydrocarbon receptor binding
O0019899molecular_functionenzyme binding
O0032991cellular_componentprotein-containing complex
O0042789biological_processmRNA transcription by RNA polymerase II
O0045120cellular_componentpronucleus
O0045893biological_processpositive regulation of DNA-templated transcription
O0051123biological_processRNA polymerase II preinitiation complex assembly
O0060261biological_processpositive regulation of transcription initiation by RNA polymerase II
O0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
O0140297molecular_functionDNA-binding transcription factor binding
Q0001091molecular_functionRNA polymerase II general transcription initiation factor binding
Q0001096molecular_functionTFIIF-class transcription factor complex binding
Q0003677molecular_functionDNA binding
Q0003723molecular_functionRNA binding
Q0005515molecular_functionprotein binding
Q0005634cellular_componentnucleus
Q0005654cellular_componentnucleoplasm
Q0005669cellular_componenttranscription factor TFIID complex
Q0005674cellular_componenttranscription factor TFIIF complex
Q0006366biological_processtranscription by RNA polymerase II
Q0006367biological_processtranscription initiation at RNA polymerase II promoter
Q0006368biological_processtranscription elongation by RNA polymerase II
Q0009615biological_processresponse to virus
Q0016251molecular_functionRNA polymerase II general transcription initiation factor activity
Q0019211molecular_functionphosphatase activator activity
Q0019903molecular_functionprotein phosphatase binding
Q0019904molecular_functionprotein domain specific binding
Q0030054cellular_componentcell junction
Q0032091biological_processnegative regulation of protein binding
Q0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
Q0032991cellular_componentprotein-containing complex
Q0043231cellular_componentintracellular membrane-bounded organelle
Q0045944biological_processpositive regulation of transcription by RNA polymerase II
Q1990841molecular_functionpromoter-specific chromatin binding
R0003677molecular_functionDNA binding
R0005515molecular_functionprotein binding
R0005634cellular_componentnucleus
R0005654cellular_componentnucleoplasm
R0005674cellular_componenttranscription factor TFIIF complex
R0006366biological_processtranscription by RNA polymerase II
R0006367biological_processtranscription initiation at RNA polymerase II promoter
R0006368biological_processtranscription elongation by RNA polymerase II
R0015630cellular_componentmicrotubule cytoskeleton
R0016251molecular_functionRNA polymerase II general transcription initiation factor activity
R0045944biological_processpositive regulation of transcription by RNA polymerase II
U0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
U0001091molecular_functionRNA polymerase II general transcription initiation factor binding
U0003677molecular_functionDNA binding
U0005515molecular_functionprotein binding
U0005634cellular_componentnucleus
U0005654cellular_componentnucleoplasm
U0005669cellular_componenttranscription factor TFIID complex
U0005672cellular_componenttranscription factor TFIIA complex
U0005737cellular_componentcytoplasm
U0005829cellular_componentcytosol
U0006366biological_processtranscription by RNA polymerase II
U0006367biological_processtranscription initiation at RNA polymerase II promoter
U0016251molecular_functionRNA polymerase II general transcription initiation factor activity
U0017025molecular_functionTBP-class protein binding
U0045944biological_processpositive regulation of transcription by RNA polymerase II
U0046982molecular_functionprotein heterodimerization activity
U0051123biological_processRNA polymerase II preinitiation complex assembly
U0060261biological_processpositive regulation of transcription initiation by RNA polymerase II
U0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
U0097550cellular_componenttranscription preinitiation complex
V0001091molecular_functionRNA polymerase II general transcription initiation factor binding
V0005515molecular_functionprotein binding
V0005634cellular_componentnucleus
V0005654cellular_componentnucleoplasm
V0005669cellular_componenttranscription factor TFIID complex
V0005672cellular_componenttranscription factor TFIIA complex
V0006366biological_processtranscription by RNA polymerase II
V0006367biological_processtranscription initiation at RNA polymerase II promoter
V0016251molecular_functionRNA polymerase II general transcription initiation factor activity
V0017025molecular_functionTBP-class protein binding
V0030054cellular_componentcell junction
V0042803molecular_functionprotein homodimerization activity
V0045944biological_processpositive regulation of transcription by RNA polymerase II
V0046982molecular_functionprotein heterodimerization activity
V0051123biological_processRNA polymerase II preinitiation complex assembly
V0060261biological_processpositive regulation of transcription initiation by RNA polymerase II
V0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
W0001113biological_processtranscription open complex formation at RNA polymerase II promoter
W0005515molecular_functionprotein binding
W0005634cellular_componentnucleus
W0005654cellular_componentnucleoplasm
W0005669cellular_componenttranscription factor TFIID complex
W0005673cellular_componenttranscription factor TFIIE complex
W0005829cellular_componentcytosol
W0006366biological_processtranscription by RNA polymerase II
W0006367biological_processtranscription initiation at RNA polymerase II promoter
W0016251molecular_functionRNA polymerase II general transcription initiation factor activity
W0046872molecular_functionmetal ion binding
X0001097molecular_functionTFIIH-class transcription factor complex binding
X0003677molecular_functionDNA binding
X0003723molecular_functionRNA binding
X0005515molecular_functionprotein binding
X0005634cellular_componentnucleus
X0005654cellular_componentnucleoplasm
X0005669cellular_componenttranscription factor TFIID complex
X0005673cellular_componenttranscription factor TFIIE complex
X0005829cellular_componentcytosol
X0006366biological_processtranscription by RNA polymerase II
X0006367biological_processtranscription initiation at RNA polymerase II promoter
X0016251molecular_functionRNA polymerase II general transcription initiation factor activity
Functional Information from PROSITE/UniProt
site_idPS00018
Number of Residues13
DetailsEF_HAND_1 EF-hand calcium-binding domain. DNDPSDYVEqdDI
ChainResidueDetails
CASP136-ILE148

site_idPS00115
Number of Residues7
DetailsRNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA
ChainResidueDetails
ATYR1593-ALA1599
ATYR1671-SER1677
ATYR1678-SER1684
ATYR1685-SER1691
ATYR1692-SER1698
ATYR1699-SER1705
ATYR1706-SER1712
ATYR1713-SER1719
ATYR1720-SER1726
ATYR1727-SER1733
ATYR1734-SER1740
ATYR1615-SER1621
ATYR1741-SER1747
ATYR1748-SER1754
ATYR1755-ASN1761
ATYR1762-ASN1768
ATYR1769-SER1775
ATYR1776-SER1782
ATYR1783-ASN1789
ATYR1790-ASN1796
ATYR1797-SER1803
ATYR1804-SER1810
ATYR1622-SER1628
ATYR1811-SER1817
ATYR1832-SER1838
ATYR1839-SER1845
ATYR1846-LYS1852
ATYR1853-SER1859
ATYR1867-LYS1873
ATYR1874-LYS1880
ATYR1881-LYS1887
ATYR1888-THR1894
ATYR1902-THR1908
ATYR1629-ASN1635
ATYR1916-LYS1922
ATYR1923-THR1929
ATYR1930-LYS1936
ATYR1937-THR1943
ATYR1944-LYS1950
ATYR1961-THR1967
ATYR1636-SER1642
ATYR1643-SER1649
ATYR1650-SER1656
ATYR1657-SER1663
ATYR1664-SER1670

site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YVCTAPH
ChainResidueDetails
ITYR112-HIS118

site_idPS00351
Number of Residues50
DetailsTFIID Transcription factor TFIID repeat signature. YnPkrFaaVImRirePRttaLIFsSGKMvctGAKseeqsrlAarkyarvV
ChainResidueDetails
OTYR192-VAL241
OTYR283-LEU332

site_idPS00446
Number of Residues41
DetailsRNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSIRRvfiaevpiiAidwVqidaNsSvlhDEfIAhRLGLIP
ChainResidueDetails
CASN32-PRO72

site_idPS00466
Number of Residues38
DetailsZF_TFIIS_1 Zinc finger TFIIS-type signature. CqkCghkeavffqSHSARaEDAmrlyyvCtaph.CghrW
ChainResidueDetails
ICYS86-TRP123

site_idPS00782
Number of Residues16
DetailsTFIIB Transcription factor TFIIB repeat signature. GRandAIASACLYIAC
ChainResidueDetails
MGLY153-CYS168
MGLY247-SER262

site_idPS01030
Number of Residues27
DetailsRNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCQECNNMLypkedkenrillyaCrnC
ChainResidueDetails
IPHE16-CYS42

site_idPS01110
Number of Residues14
DetailsRNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPEHvvMtkEE
ChainResidueDetails
EHIS142-GLU155

site_idPS01111
Number of Residues15
DetailsRNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARvLGtRAlQ
ChainResidueDetails
FTHR58-GLN72

site_idPS01112
Number of Residues10
DetailsRNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IIPVrCFTCG
ChainResidueDetails
JILE2-GLY11

site_idPS01154
Number of Residues32
DetailsRNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. InkEdHTLgNiIksqLlkdpqVlfagYkvpHP
ChainResidueDetails
KILE35-PRO66

site_idPS01166
Number of Residues13
DetailsRNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
ChainResidueDetails
BGLY932-THR944

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues25
DetailsZN_FING: C4-type => ECO:0000255
ChainResidueDetails
ICYS17-CYS42
UARG344
QGLU517
OASN257
OARG294

site_idSWS_FT_FI2
Number of Residues42
DetailsZN_FING: TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
ChainResidueDetails
IGLU82-THR124
WCYS132
WCYS154
WCYS157

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU10145
ChainResidueDetails
ICYS17
ICYS20
ICYS39
ICYS42

site_idSWS_FT_FI4
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00472
ChainResidueDetails
ICYS86
MTHR284
MARG286
MARG290
ICYS89
ICYS114
ICYS119
MLYS189
MLYS196
MARG248
MLYS272
MALA281

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: N-acetylmethionine => ECO:0000250|UniProtKB:P36954
ChainResidueDetails
IMET1
USER321

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:20068231
ChainResidueDetails
QSER221

site_idSWS_FT_FI7
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:21406692
ChainResidueDetails
QTHR331

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163
ChainResidueDetails
QSER377
QSER431

site_idSWS_FT_FI9
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648
ChainResidueDetails
QSER380
QSER381
QSER436
QSER449

site_idSWS_FT_FI10
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:10428810, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163
ChainResidueDetails
QSER385

site_idSWS_FT_FI11
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0000269|PubMed:10428810, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163
ChainResidueDetails
QTHR389

site_idSWS_FT_FI12
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692
ChainResidueDetails
QSER391

site_idSWS_FT_FI13
Number of Residues1
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
QLYS407

site_idSWS_FT_FI14
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163
ChainResidueDetails
QSER433

site_idSWS_FT_FI15
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648
ChainResidueDetails
QTHR446

226707

PDB entries from 2024-10-30

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