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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9KD9

The structure of RNA polymerase II elongation complex paused at N-5 state by actinomycin D.

Functional Information from PROSITE/UniProt
site_idPS00115
Number of Residues7
DetailsRNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA
ChainResidueDetails
ATYR1549-ALA1555
ATYR1612-SER1618
ATYR1619-SER1625
ATYR1626-SER1632
ATYR1633-SER1639
ATYR1640-SER1646
ATYR1647-SER1653
ATYR1654-ALA1660
ATYR1661-SER1667
ATYR1668-SER1674
ATYR1675-SER1681
ATYR1556-SER1562
ATYR1682-SER1688
ATYR1689-ASN1695
ATYR1696-SER1702
ATYR1563-SER1569
ATYR1570-SER1576
ATYR1577-SER1583
ATYR1584-SER1590
ATYR1591-SER1597
ATYR1598-SER1604
ATYR1605-SER1611
site_idPS00446
Number of Residues41
DetailsRNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP
ChainResidueDetails
CASN31-PRO71
site_idPS00466
Number of Residues36
DetailsZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF
ChainResidueDetails
ICYS75-PHE110
site_idPS01030
Number of Residues27
DetailsRNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCRDCNNMLypredkennrllfeCrtC
ChainResidueDetails
IPHE6-CYS32
site_idPS01110
Number of Residues14
DetailsRNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE
ChainResidueDetails
EHIS147-GLU160
site_idPS01111
Number of Residues15
DetailsRNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ
ChainResidueDetails
FTHR86-GLN100
site_idPS01112
Number of Residues10
DetailsRNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG
ChainResidueDetails
JILE2-GLY11
site_idPS01154
Number of Residues32
DetailsRNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP
ChainResidueDetails
KPHE35-PRO66
site_idPS01166
Number of Residues13
DetailsRNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
ChainResidueDetails
BGLY977-THR989
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues17
DetailsRegion: {"description":"Rudder loop"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues12
DetailsRegion: {"description":"Bridging helix"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues11
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23151482","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25652824","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4BBR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V1M","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues5
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"32142654","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues42
DetailsZinc finger: {"description":"C4-type"}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues13
DetailsBinding site: {}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues21
DetailsRegion: {"description":"Leucine-zipper"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues23
DetailsRegion: {"description":"Non-specific ssDNA binding","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues25
DetailsZinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues40
DetailsZinc finger: {"description":"TFIIS-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00472","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10145","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11313498","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11805306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11313499","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00472","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11313498","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11805306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11313499","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1TWF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues1
DetailsM-CSA 788
ChainResidueDetails
BASP837metal ligand
AASP483metal ligand
AASP485metal ligand

244349

PDB entries from 2025-11-05

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