8JH2

RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
F [auth D]SCOP2B SuperfamilyHRDC-like8078369 3000132 SCOP2B (2022-06-29)
N [auth L]SCOP2B SuperfamilyRNA polymerase subunits8080893 3001823 SCOP2B (2022-06-29)
U [auth a]SCOP2B SuperfamilyCore histone-like8070527 3001387 SCOP2B (2022-06-29)
Y [auth e]SCOP2B SuperfamilyCore histone-like8070527 3001387 SCOP2B (2022-06-29)
V [auth b]SCOP2B SuperfamilyCore histone-like8070545 3001387 SCOP2B (2022-06-29)
Z [auth f]SCOP2B SuperfamilyCore histone-like8070545 3001387 SCOP2B (2022-06-29)
AA [auth g]SCOP2B SuperfamilyCore histone-like8039342 3001387 SCOP2B (2022-06-29)
W [auth c]SCOP2B SuperfamilyCore histone-like8039342 3001387 SCOP2B (2022-06-29)
J [auth H]SCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like8093395 3002702 SCOP2B (2022-06-29)
J [auth H]SCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like8078385 3002702 SCOP2B (2022-06-29)
L [auth J]SCOP2B SuperfamilyRNA polymerase subunit RPB108063366 3001213 SCOP2B (2022-06-29)
M [auth K]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8080724 3001655 SCOP2B (2022-06-29)
O [auth M]SCOP2B SuperfamilyZinc beta-ribbon8097424 3001238 SCOP2B (2022-06-29)
H [auth F]SCOP2B SuperfamilyRPB6/omega subunit-like8078373 3000189 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth A]PF00623e8jh2A9 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00623ECOD (1.6)
C [auth A]PF00623e8jh2A7 A: a+b two layersX: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymeraseF: PF00623ECOD (1.6)
C [auth A]PF04990e8jh2A3 A: a+b two layersX: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunitF: PF04990ECOD (1.6)
C [auth A]F_UNCLASSIFIEDe8jh2A1 A: a+b two layersX: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunitF: F_UNCLASSIFIEDECOD (1.6)
C [auth A]PF04997e8jh2A5 A: a+b complex topologyX: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)T: N-terminal domain in RNA-polymerase beta-prime subunitF: PF04997ECOD (1.6)
C [auth A]PF04998e8jh2A8 A: a+b complex topologyX: central helical domain in RNA-polymerase beta-prime subunit (From Topology)H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)T: central helical domain in RNA-polymerase beta-prime subunitF: PF04998ECOD (1.6)
C [auth A]PF04992e8jh2A2 A: a+b complex topologyX: helical domain in yeast RNA-polymerasesH: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)T: third helical domain in yeast RNA-polymerase II beta-prime subunitF: PF04992ECOD (1.6)
C [auth A]PF04998,PF05000e8jh2A4 A: a+b complex topologyX: second helical domain in RNA-polymerase beta-prime subunit (From Topology)H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)T: second helical domain in RNA-polymerase beta-prime subunitF: PF04998,PF05000ECOD (1.6)
C [auth A]PF04983e8jh2A6 A: a+b complex topologyX: first helical domain in RNA-polymerase beta-prime subunit (From Topology)H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)T: first helical domain in RNA-polymerase beta-prime subunitF: PF04983ECOD (1.6)
D [auth B]PF00562e8jh2B5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00562ECOD (1.6)
D [auth B]PF00562e8jh2B1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PF00562ECOD (1.6)
D [auth B]PF04563,PF04565e8jh2B2 A: a+b complex topologyX: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: N-terminal domain in beta subunit of DNA dependent RNA-polymeraseF: PF04563,PF04565ECOD (1.6)
D [auth B]PF04561e8jh2B7 A: a+b complex topologyX: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: insertion domain in beta subunit of DNA dependent RNA-polymeraseF: PF04561ECOD (1.6)
D [auth B]PF00562,PF04567e8jh2B4 A: a+b complex topologyX: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: barrel domain in beta subunit of DNA dependent RNA-polymeraseF: PF00562,PF04567ECOD (1.6)
D [auth B]PF00562,PF04560e8jh2B6 A: a+b complex topologyX: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: C-terminal domain in beta subunit of DNA dependent RNA-polymeraseF: PF00562,PF04560ECOD (1.6)
D [auth B]PF04566e8jh2B3 A: a+b complex topologyX: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)T: inserted a+b domain in yeast RNA polymerase beta subunitF: PF04566ECOD (1.6)
E [auth C]PF01193e8jh2C1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
E [auth C]PF01000e8jh2C2 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: PF01000ECOD (1.6)
F [auth D]PF03874e8jh2D1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: PF03874ECOD (1.6)
I [auth G]PF00575e8jh2G1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00575ECOD (1.6)
I [auth G]PF03876e8jh2G2 A: a+b two layersX: Dodecin subunit-likeH: Flavin-binding protein dodecin-like (From Topology)T: Flavin-binding protein dodecin-likeF: PF03876ECOD (1.6)
N [auth L]PF03604e8jh2L1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF03604ECOD (1.6)
U [auth a]PF00125e8jh2a1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
Y [auth e]PF00125e8jh2e1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
V [auth b]PF15511e8jh2b1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF15511ECOD (1.6)
Z [auth f]PF15511e8jh2f1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF15511ECOD (1.6)
AA [auth g]PF00125,PF16211e8jh2g1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125,PF16211ECOD (1.6)
W [auth c]PF00125,PF16211e8jh2c1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125,PF16211ECOD (1.6)
BA [auth h]PF00125e8jh2h1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
X [auth d]PF00125e8jh2d1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
J [auth H]PF03870e8jh2H1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF03870ECOD (1.6)
K [auth I]PF01096e8jh2I1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01096ECOD (1.6)
K [auth I]PF02150e8jh2I2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF02150ECOD (1.6)
L [auth J]PF01194e8jh2J1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: PF01194ECOD (1.6)
M [auth K]PF13656e8jh2K1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF13656ECOD (1.6)
O [auth M]PF05129e8jh2M1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF05129ECOD (1.6)
S [auth V]PF06093e8jh2V1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF06093ECOD (1.6)
T [auth W]PF00467e8jh2W2 A: beta barrelsX: SH3H: SH3T: SH3F: PF00467ECOD (1.6)
T [auth W]PF03439e8jh2W1 A: a+b two layersX: Alpha-beta plaitsH: N-utilization substance G protein NusG, N-terminal domain (From Topology)T: N-utilization substance G protein NusG, N-terminal domainF: PF03439ECOD (1.6)
G [auth E]PF01191e8jh2E1 A: a+b two layersX: RPB5-like RNA polymerase subunit (From Topology)H: RPB5-like RNA polymerase subunit (From Topology)T: RPB5-like RNA polymerase subunitF: PF01191ECOD (1.6)
G [auth E]PF03871e8jh2E2 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Eukaryotic RPB5 N-terminal domain (From Topology)T: Eukaryotic RPB5 N-terminal domainF: PF03871ECOD (1.6)
H [auth F]PF01192e8jh2F1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: PF01192ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 0]DNA (40-MER)---
C [auth A]DNA-directed RNA polymerase subunit
D [auth B]DNA-directed RNA polymerase subunit beta
E [auth C]RNA polymerase II third largest subunit B44, part of central core
F [auth D]RNA polymerase II subunit B32
I [auth G]RNA polymerase II subunit
N [auth L]RNA polymerase subunit ABC10-alpha
R [auth T]DNA (218-MER)---
U [auth a],
Y [auth e]
Histone H3.3
V [auth b],
Z [auth f]
Histone H4
AA [auth g],
W [auth c]
Histone H2A type 1-B/E
BA [auth h],
X [auth d]
Histone H2B type 1-J
J [auth H]DNA-directed RNA polymerases I, II, and III subunit RPABC3
K [auth I]DNA-directed RNA polymerase subunit
L [auth J]RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
M [auth K]RNA polymerase II subunit B12.5
O [auth M]Transcription elongation factor 1 homolog -
P [auth N]DNA (218-MER)---
Q [auth P]RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')---
S [auth V]Transcription elongation factor SPT4
B [auth 1]DNA (40-MER)---
T [auth W]Transcription elongation factor SPT5
G [auth E]RNA polymerase subunit ABC27
H [auth F]RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth A]IPR007066RNA polymerase Rpb1, domain 3Domain
C [auth A]IPR007081RNA polymerase Rpb1, domain 5Domain
C [auth A]IPR007073RNA polymerase Rpb1, domain 7Domain
C [auth A]IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
C [auth A]IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
C [auth A]IPR007075RNA polymerase Rpb1, domain 6Domain
C [auth A]IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
C [auth A]IPR007083RNA polymerase Rpb1, domain 4Domain
C [auth A]IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
C [auth A]IPR000722RNA polymerase, alpha subunitDomain
C [auth A]IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
C [auth A]IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
C [auth A]IPR006592RNA polymerase, N-terminalDomain
C [auth A]IPR007080RNA polymerase Rpb1, domain 1Domain
D [auth B]IPR007642RNA polymerase Rpb2, domain 2Domain
D [auth B]IPR015712DNA-directed RNA polymerase, subunit 2Family
D [auth B]IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
D [auth B]IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
D [auth B]IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
D [auth B]IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
D [auth B]IPR007645RNA polymerase Rpb2, domain 3Domain
D [auth B]IPR007646RNA polymerase Rpb2, domain 4Domain
D [auth B]IPR007647RNA polymerase Rpb2, domain 5Domain
D [auth B]IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
D [auth B]IPR007644RNA polymerase, beta subunit, protrusionDomain
D [auth B]IPR007641RNA polymerase Rpb2, domain 7Domain
E [auth C]IPR011262DNA-directed RNA polymerase, insert domainDomain
E [auth C]IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
E [auth C]IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
E [auth C]IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
E [auth C]IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
E [auth C]IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
F [auth D]IPR005574RNA polymerase subunit Rpb4/RPC9Family
F [auth D]IPR010997HRDC-like superfamilyHomologous Superfamily
F [auth D]IPR006590RNA polymerase Rpb4/RPC9, coreDomain
F [auth D]IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
F [auth D]IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
I [auth G]IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
I [auth G]IPR003029S1 domainDomain
I [auth G]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
I [auth G]IPR045113RNA polymerase subunit Rpb7-likeFamily
I [auth G]IPR005576RNA polymerase Rpb7-like , N-terminalDomain
N [auth L]IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
N [auth L]IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
N [auth L]IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
U [auth a],
Y [auth e]
IPR009072Histone-foldHomologous Superfamily
U [auth a],
Y [auth e]
IPR007125Histone H2A/H2B/H3Domain
U [auth a],
Y [auth e]
IPR000164Histone H3/CENP-AFamily
V [auth b],
Z [auth f]
IPR009072Histone-foldHomologous Superfamily
V [auth b],
Z [auth f]
IPR035425CENP-T/Histone H4, histone foldDomain
V [auth b],
Z [auth f]
IPR001951Histone H4Family
V [auth b],
Z [auth f]
IPR019809Histone H4, conserved siteConserved Site
V [auth b],
Z [auth f]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
AA [auth g],
W [auth c]
IPR009072Histone-foldHomologous Superfamily
AA [auth g],
W [auth c]
IPR007125Histone H2A/H2B/H3Domain
AA [auth g],
W [auth c]
IPR002119Histone H2AFamily
AA [auth g],
W [auth c]
IPR032454Histone H2A, C-terminal domainDomain
AA [auth g],
W [auth c]
IPR032458Histone H2A conserved siteConserved Site
BA [auth h],
X [auth d]
IPR009072Histone-foldHomologous Superfamily
BA [auth h],
X [auth d]
IPR007125Histone H2A/H2B/H3Domain
BA [auth h],
X [auth d]
IPR000558Histone H2BFamily
J [auth H]IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
J [auth H]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
K [auth I]IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
K [auth I]IPR001222Zinc finger, TFIIS-typeDomain
K [auth I]IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
K [auth I]IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
K [auth I]IPR001529DNA-directed RNA polymerase, M/15kDa subunitDomain
L [auth J]IPR023580RNA polymerase subunit RPB10Homologous Superfamily
L [auth J]IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
L [auth J]IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
M [auth K]IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
M [auth K]IPR037685RNA polymerase RBP11Family
M [auth K]IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
M [auth K]IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
M [auth K]IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
O [auth M]IPR007808Transcription elongation factor 1Family
O [auth M]IPR038567Transcription elongation factor 1 superfamilyHomologous Superfamily
S [auth V]IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
S [auth V]IPR038510Spt4 superfamilyHomologous Superfamily
S [auth V]IPR009287Transcription initiation Spt4Family
S [auth V]IPR022800Spt4/RpoE2 zinc fingerDomain
T [auth W]IPR036735NusG, N-terminal domain superfamilyHomologous Superfamily
T [auth W]IPR041976Spt5, KOW domain repeat 3Domain
T [auth W]IPR039385NGN domain, eukaryoticDomain
T [auth W]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
T [auth W]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
T [auth W]IPR041973Spt5, KOW domain repeat 1Domain
T [auth W]IPR022581Spt5 transcription elongation factor, N-terminalDomain
T [auth W]IPR005100NGN domainDomain
T [auth W]IPR041977Spt5, KOW domain repeat 4Domain
T [auth W]IPR017071Transcription elongation factor Spt5, eukaryoteFamily
T [auth W]IPR005824KOWDomain
T [auth W]IPR041975Spt5, KOW domain repeat 2Domain
T [auth W]IPR041978Spt5, KOW domain repeat 5Domain
T [auth W]IPR039659Transcription elongation factor SPT5Family
G [auth E]IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
G [auth E]IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
G [auth E]IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
G [auth E]IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
G [auth E]IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
G [auth E]IPR005571RNA polymerase, Rpb5, N-terminalDomain
H [auth F]IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
H [auth F]IPR028363DNA-directed RNA polymerase, subunit RPB6Family
H [auth F]IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
H [auth F]IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
H [auth F]IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
U [auth a],
Y [auth e]
PharosP84243
V [auth b],
Z [auth f]
PharosP62805
AA [auth g],
W [auth c]
PharosP04908
BA [auth h],
X [auth d]
PharosP06899