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X - Possible homology level

H - Homology level

T - Topology level

F - Family level

* - Provisional representative


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Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

alpha bundlesalpha-helix bundles with mainly parallel helices

alpha superhelicesrepeating alpha-helix hairpins form a superhelix

alpha duplicates or obligate multimersalpha duplicates or monomers associate together to form a compact domain

alpha complex topologyalpha domain with complex and unique topology that cannot be described as array or bundle or superhelix

beta barrelssingle beta-sheet folded upon itself to form a barrel

beta meanderssingle beta-sheet with mainly meander topology

beta sandwichestwo beta-sheets stacked together to form a sandwich

beta duplicates or obligate multimersbeta duplicates or monomers associate together to form a compact domain

beta complex topologybeta domains with complex and unique topology that cannot be described as barrel or sandwich or meander

a+b two layersone alpha-helix layer and one beta-sheet layer

X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
F: RNA_pol_Rpb1_5

PF04998

Representatives:

e1twfA2[A:1113-1141,A:1273-1330] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT ; X-RAY DIFFRACTION 2.3Å

e7f4gA8[A:1136-1162,A:1300-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e8b3fA8[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH

; ELECTRON MICROSCOPY

e8oevA1[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8oewA1[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8of0A3[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4bA9[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4cA3[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4dA4[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4eA6[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e5ip7A6[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.520Å

e5ip9A4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.450Å

e5fywA1[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 ; ELECTRON MICROSCOPY

e5fz5A6[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 ; ELECTRON MICROSCOPY

e5iy6A7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iy7A5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iy8A4[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iy9A7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iyaA5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iybA4[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iycA8[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5iydA5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e3h0gM4[M:1116-1144,M:1279-1336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit rpb1 ; X-RAY DIFFRACTION 3.650Å

e1i50A4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT ; X-RAY DIFFRACTION 2.8Å

e2nvyA4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT ; X-RAY DIFFRACTION 3.4Å

e4bxxA6[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 ; X-RAY DIFFRACTION 3.28Å

e3cqzA4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 ; X-RAY DIFFRACTION 2.8Å

e5flmA5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE ; ELECTRON MICROSCOPY

e5oikA7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5oqjA9[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e5oqmA7[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e6blpA7[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.2Å

e6bm2A3[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.4Å

e6bm4A3[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 2.95Å

e6bqfA3[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.35Å

e6exvA5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 ; ELECTRON MICROSCOPY

e6gmlA8[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e6gykA4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e6gylA4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e6gymA4[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7b0yA6[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7lbmA6[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7edxo3[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7eg7o9[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7eg8o1[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7eg9o4[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7egao2[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7egbo8[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7nvrA2[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7nvsA7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvtA7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvuA7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvyA6[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvzA2[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nw0A5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e6xreA8[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7egco4[o:1136-1164,o:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7okxA9[A:1136-1164,A:1299-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7nkxA9[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e6gmhA8[A:1135-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7okyA9[A:1136-1164,A:1299-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7ol0A8[A:1135-1163,A:1300-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7oznA8[A:1136-1164,A:1299-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7oznM8[M:1136-1164,M:1299-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7ozoA8[A:1136-1164,A:1299-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozoM8[M:1136-1164,M:1299-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozpA8[A:1136-1164,A:1297-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozpM8[M:1136-1164,M:1297-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7pksA9[A:1136-1163,A:1300-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7oobA5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7ml0A9[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml1A8[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml2A2[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml4A2[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ripA3[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.270Å

e7riqA9[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 2.960Å

e7riwA2[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.17Å

e7rixA6[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.3Å

e7riyA3[A:1113-1141,A:1273-1330] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.630Å

e7oo3A5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7oopA8[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7opcA3[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7opdA7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zwdA2[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7zx7A6[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7zx8A7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8bvwA2[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8byqA8[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8bz1A9[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ycx14[1:1136-1164,1:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4 ; ELECTRON MICROSCOPY

e8p4fA5[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8a40A2[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8b3dA4[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH

; ELECTRON MICROSCOPY

e8oeuA3[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4aA7[A:1136-1164,A:1298-1360] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

F: Unmapped domains

Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.

X: LuxS, MPP, ThrRS/AlaRS common domain

looks like an elaborated ferredoxin

X: ClpS-like

contains a HTH motif

a+b three layersone mainly antiparallel beta-sheet layer sandwiched between two alpha-helix layers

a+b four layerstwo beta-sheet layers sandwiched between two alpha-helix layers

a+b complex topologyalpha and beta domain with complex and unique topology that cannot be described in layers

a+b duplicates or obligate multimersalpha and beta duplicates or monomers associated together to form a compact domain

a/b barrelsrepeating beta-alpha units form a barrel

a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers

mixed a+b and a/balpha and beta domain consists of both a+b and a/b regions

few secondary structure elementsstabilized by cofactors or disulfides

extended segmentsextended, non-globular segments, frequently bind to other proteins to form complexes