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8A3Y

Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0000428cellular_componentDNA-directed RNA polymerase complex
A0001054molecular_functionRNA polymerase I activity
A0001055molecular_functionRNA polymerase II activity
A0001056molecular_functionRNA polymerase III activity
A0001057molecular_functionRNA polymerase IV activity
A0001058molecular_functionRNA polymerase V activity
A0001059biological_processtranscription by RNA polymerase IV
A0001060biological_processtranscription by RNA polymerase V
A0001065molecular_functionmitochondrial single subunit type RNA polymerase activity
A0001066molecular_functionplastid single subunit type RNA polymerase activity
A0003677molecular_functionDNA binding
A0005634cellular_componentnucleus
A0006360biological_processtranscription by RNA polymerase I
A0006383biological_processtranscription by RNA polymerase III
A0006390biological_processmitochondrial transcription
A0016779molecular_functionnucleotidyltransferase activity
A0031981cellular_componentnuclear lumen
A0042793biological_processplastid transcription
A0046872molecular_functionmetal ion binding
B0000428cellular_componentDNA-directed RNA polymerase complex
B0000781cellular_componentchromosome, telomeric region
B0001054molecular_functionRNA polymerase I activity
B0001055molecular_functionRNA polymerase II activity
B0001056molecular_functionRNA polymerase III activity
B0001057molecular_functionRNA polymerase IV activity
B0001058molecular_functionRNA polymerase V activity
B0001059biological_processtranscription by RNA polymerase IV
B0001060biological_processtranscription by RNA polymerase V
B0001065molecular_functionmitochondrial single subunit type RNA polymerase activity
B0001066molecular_functionplastid single subunit type RNA polymerase activity
B0001172biological_processRNA-templated transcription
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
B0006360biological_processtranscription by RNA polymerase I
B0006366biological_processtranscription by RNA polymerase II
B0006383biological_processtranscription by RNA polymerase III
B0006390biological_processmitochondrial transcription
B0016779molecular_functionnucleotidyltransferase activity
B0034062molecular_function5'-3' RNA polymerase activity
B0042793biological_processplastid transcription
B0046872molecular_functionmetal ion binding
C0000428cellular_componentDNA-directed RNA polymerase complex
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005665cellular_componentRNA polymerase II, core complex
C0005829cellular_componentcytosol
C0006366biological_processtranscription by RNA polymerase II
E0001054molecular_functionRNA polymerase I activity
E0001055molecular_functionRNA polymerase II activity
E0001056molecular_functionRNA polymerase III activity
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005665cellular_componentRNA polymerase II, core complex
E0005666cellular_componentRNA polymerase III complex
E0005736cellular_componentRNA polymerase I complex
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
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005665cellular_componentRNA polymerase II, core complex
F0005666cellular_componentRNA polymerase III complex
F0005736cellular_componentRNA polymerase I complex
F0006366biological_processtranscription by RNA polymerase II
G0000428cellular_componentDNA-directed RNA polymerase complex
G0005634cellular_componentnucleus
G0006352biological_processDNA-templated transcription initiation
H0000428cellular_componentDNA-directed RNA polymerase complex
H0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
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
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
I0006366biological_processtranscription by RNA polymerase II
I0006367biological_processtranscription initiation at RNA polymerase II promoter
I0046872molecular_functionmetal ion binding
J0000428cellular_componentDNA-directed RNA polymerase complex
J0046872molecular_functionmetal ion binding
K0000428cellular_componentDNA-directed RNA polymerase complex
K0005634cellular_componentnucleus
K0005665cellular_componentRNA polymerase II, core complex
L0005634cellular_componentnucleus
L0046872molecular_functionmetal ion binding
Q0000122biological_processnegative regulation of transcription by RNA polymerase II
Q0000791cellular_componenteuchromatin
Q0000993molecular_functionRNA polymerase II complex binding
Q0001650cellular_componentfibrillar center
Q0001711biological_processendodermal cell fate commitment
Q0001826biological_processinner cell mass cell differentiation
Q0001829biological_processtrophectodermal cell differentiation
Q0001832biological_processblastocyst growth
Q0001835biological_processblastocyst hatching
Q0005515molecular_functionprotein binding
Q0005634cellular_componentnucleus
Q0005654cellular_componentnucleoplasm
Q0005813cellular_componentcentrosome
Q0006325biological_processchromatin organization
Q0006368biological_processtranscription elongation by RNA polymerase II
Q0007259biological_processcell surface receptor signaling pathway via JAK-STAT
Q0016055biological_processWnt signaling pathway
Q0016593cellular_componentCdc73/Paf1 complex
Q0016607cellular_componentnuclear speck
Q0019827biological_processstem cell population maintenance
Q0031124biological_processmRNA 3'-end processing
Q0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
Q0042169molecular_functionSH2 domain binding
Q0045638biological_processnegative regulation of myeloid cell differentiation
Q0045814biological_processnegative regulation of gene expression, epigenetic
Q0045944biological_processpositive regulation of transcription by RNA polymerase II
Q0070102biological_processinterleukin-6-mediated signaling pathway
Q0071222biological_processcellular response to lipopolysaccharide
Q1990269molecular_functionRNA polymerase II C-terminal domain phosphoserine binding
U0000122biological_processnegative regulation of transcription by RNA polymerase II
U0000791cellular_componenteuchromatin
U0000993molecular_functionRNA polymerase II complex binding
U0001650cellular_componentfibrillar center
U0001711biological_processendodermal cell fate commitment
U0001826biological_processinner cell mass cell differentiation
U0001829biological_processtrophectodermal cell differentiation
U0001832biological_processblastocyst growth
U0001835biological_processblastocyst hatching
U0005515molecular_functionprotein binding
U0005634cellular_componentnucleus
U0005654cellular_componentnucleoplasm
U0005813cellular_componentcentrosome
U0006325biological_processchromatin organization
U0006368biological_processtranscription elongation by RNA polymerase II
U0007259biological_processcell surface receptor signaling pathway via JAK-STAT
U0016055biological_processWnt signaling pathway
U0016593cellular_componentCdc73/Paf1 complex
U0016607cellular_componentnuclear speck
U0019827biological_processstem cell population maintenance
U0031124biological_processmRNA 3'-end processing
U0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
U0042169molecular_functionSH2 domain binding
U0045638biological_processnegative regulation of myeloid cell differentiation
U0045814biological_processnegative regulation of gene expression, epigenetic
U0045944biological_processpositive regulation of transcription by RNA polymerase II
U0070102biological_processinterleukin-6-mediated signaling pathway
U0071222biological_processcellular response to lipopolysaccharide
U1990269molecular_functionRNA polymerase II C-terminal domain phosphoserine binding
W0000791cellular_componenteuchromatin
W0005515molecular_functionprotein binding
W0005634cellular_componentnucleus
W0005654cellular_componentnucleoplasm
W0005737cellular_componentcytoplasm
W0005829cellular_componentcytosol
W0006368biological_processtranscription elongation by RNA polymerase II
W0016055biological_processWnt signaling pathway
W0016593cellular_componentCdc73/Paf1 complex
W0045638biological_processnegative regulation of myeloid cell differentiation
W0055087cellular_componentSki complex
W0070478biological_processnuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
W0072344biological_processrescue of stalled ribosome
X0000122biological_processnegative regulation of transcription by RNA polymerase II
X0000781cellular_componentchromosome, telomeric region
X0000993molecular_functionRNA polymerase II complex binding
X0001558biological_processregulation of cell growth
X0001711biological_processendodermal cell fate commitment
X0005515molecular_functionprotein binding
X0005634cellular_componentnucleus
X0005654cellular_componentnucleoplasm
X0005829cellular_componentcytosol
X0006357biological_processregulation of transcription by RNA polymerase II
X0006368biological_processtranscription elongation by RNA polymerase II
X0008285biological_processnegative regulation of cell population proliferation
X0016055biological_processWnt signaling pathway
X0016593cellular_componentCdc73/Paf1 complex
X0019827biological_processstem cell population maintenance
X0030177biological_processpositive regulation of Wnt signaling pathway
X0031124biological_processmRNA 3'-end processing
X0031442biological_processpositive regulation of mRNA 3'-end processing
X0031648biological_processprotein destabilization
X0032968biological_processpositive regulation of transcription elongation by RNA polymerase II
X0043066biological_processnegative regulation of apoptotic process
X0045638biological_processnegative regulation of myeloid cell differentiation
X0045944biological_processpositive regulation of transcription by RNA polymerase II
X0048147biological_processnegative regulation of fibroblast proliferation
X0050680biological_processnegative regulation of epithelial cell proliferation
X0071222biological_processcellular response to lipopolysaccharide
X1902808biological_processpositive regulation of cell cycle G1/S phase transition
X2000134biological_processnegative regulation of G1/S transition of mitotic cell cycle
Y0000993molecular_functionRNA polymerase II complex binding
Y0005634cellular_componentnucleus
Y0006368biological_processtranscription elongation by RNA polymerase II
Y0032044cellular_componentDSIF complex
Y0034244biological_processnegative regulation of transcription elongation by RNA polymerase II
Y0046872molecular_functionmetal ion binding
Z0000122biological_processnegative regulation of transcription by RNA polymerase II
Z0003682molecular_functionchromatin binding
Z0003723molecular_functionRNA binding
Z0003729molecular_functionmRNA binding
Z0005515molecular_functionprotein binding
Z0005634cellular_componentnucleus
Z0005654cellular_componentnucleoplasm
Z0006368biological_processtranscription elongation by RNA polymerase II
Z0016239biological_processpositive regulation of macroautophagy
Z0019899molecular_functionenzyme binding
Z0032044cellular_componentDSIF complex
Z0032785biological_processnegative regulation of DNA-templated transcription, elongation
Z0032786biological_processpositive regulation of DNA-templated transcription, elongation
Z0034243biological_processregulation of transcription elongation by RNA polymerase II
Z0045944biological_processpositive regulation of transcription by RNA polymerase II
Z0046982molecular_functionprotein heterodimerization activity
a0000786cellular_componentnucleosome
a0003677molecular_functionDNA binding
a0005515molecular_functionprotein binding
a0005634cellular_componentnucleus
a0005654cellular_componentnucleoplasm
a0005694cellular_componentchromosome
b0000786cellular_componentnucleosome
b0003677molecular_functionDNA binding
b0005515molecular_functionprotein binding
b0005634cellular_componentnucleus
b0005694cellular_componentchromosome
e0000786cellular_componentnucleosome
e0003677molecular_functionDNA binding
e0005515molecular_functionprotein binding
e0005634cellular_componentnucleus
e0005654cellular_componentnucleoplasm
e0005694cellular_componentchromosome
f0000786cellular_componentnucleosome
f0003677molecular_functionDNA binding
f0005515molecular_functionprotein binding
f0005634cellular_componentnucleus
f0005694cellular_componentchromosome
Functional Information from PROSITE/UniProt
site_idPS00018
Number of Residues13
DetailsEF_HAND_1 EF-hand calcium-binding domain. DNDPSDYVEqdDI
ChainResidueDetails
CASP136-ILE148

site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
cALA21-VAL27

site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
fGLY14-HIS18

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_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
eLYS14-LEU20

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
dARG89-GLY111

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_idPS00678
Number of Residues15
DetailsWD_REPEATS_1 Trp-Asp (WD) repeats signature. AASSslDaHIRLWDL
ChainResidueDetails
WALA79-LEU93

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
ePRO66-ILE74

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
fLYS16-LYS20
eARG2
eARG17

site_idSWS_FT_FI2
Number of Residues42
DetailsZN_FING: TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472
ChainResidueDetails
IGLU82-THR124
fSER1
YCYS33
YCYS36

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
ICYS89
ICYS114
ICYS119

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: N-acetylmethionine => ECO:0000250|UniProtKB:P36954
ChainResidueDetails
IMET1
bLYS16
bLYS44
bLYS79
fLYS8
fLYS16
fLYS44
fLYS79

site_idSWS_FT_FI6
Number of Residues4
DetailsMOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bLYS12
USER-94
bLYS20
fLYS12
fLYS20
QSER1085
USER-140
USER-138
USER-136
USER-98

site_idSWS_FT_FI7
Number of Residues4
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bLYS31
bLYS91
fLYS31
fLYS91

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphoserine; by PAK2 => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bSER47
fSER47
USER-82
USER-77

site_idSWS_FT_FI9
Number of Residues4
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bTYR51
bTYR88
fTYR51
fTYR88

site_idSWS_FT_FI10
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bLYS59
eLYS64
fLYS59
aLYS27
aLYS36
aLYS64
eLYS18
eLYS23
eLYS27
eLYS36

site_idSWS_FT_FI11
Number of Residues2
DetailsMOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bLYS77
USER220
fLYS77
QSER1333
QSER1391
QSER1399
USER14
USER151
USER154
USER212

site_idSWS_FT_FI12
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
bLYS31
fLYS31

site_idSWS_FT_FI13
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
aLYS37
bLYS91
QSER1358
fLYS91
USER171
USER179

site_idSWS_FT_FI14
Number of Residues2
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aTYR41
eTYR41

site_idSWS_FT_FI15
Number of Residues4
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228
ChainResidueDetails
aLYS56
aLYS79
eLYS56
eLYS79

site_idSWS_FT_FI16
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aSER57
eSER57

site_idSWS_FT_FI17
Number of Residues4
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aTHR80
aTHR107
eTHR80
eTHR107

site_idSWS_FT_FI18
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243
ChainResidueDetails
aSER86
eSER86

site_idSWS_FT_FI19
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aLYS115
eLYS115
USER294
USER617

site_idSWS_FT_FI20
Number of Residues2
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aLYS122
eLYS122

site_idSWS_FT_FI21
Number of Residues2
DetailsLIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
aCYS110
eCYS110

site_idSWS_FT_FI22
Number of Residues2
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569
ChainResidueDetails
QTYR1785
UTYR613

site_idSWS_FT_FI23
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692
ChainResidueDetails
QSER1786
QSER1787
USER614
USER615

site_idSWS_FT_FI24
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648
ChainResidueDetails
QSER1793
USER621

site_idSWS_FT_FI25
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332
ChainResidueDetails
QTHR1808
UTHR636

site_idSWS_FT_FI26
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
QSER1809
USER637

site_idSWS_FT_FI27
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18318008, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
QSER1837
USER665

227344

PDB entries from 2024-11-13

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