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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

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

X: helical domain in yeast RNA-polymerases
H: third helical domain in yeast RNA-polymerase II beta-prime subunit
T: third helical domain in yeast RNA-polymerase II beta-prime subunit
F: RNA_pol_Rpb1_6

PF04992

Representatives:

e1twfA11[A:872-1059] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7egbo2[o:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7nvrA3[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7nvsA6[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvtA3[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvuA9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvyA9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvzA9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nw0A7[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e6xreA9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7kedA7[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.550Å

e7o4iA9[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7egco9[o:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7b7uA2[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7nkyA7[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7keeA6[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.410Å

e7kefA1[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 3.890Å

e7o4jA4[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7o72A5[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7o73A3[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7o75A8[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7f4gA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7okxA5[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7nkxA5[A:872-1060] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e6gmhA5[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7okyA5[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7ol0A5[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7oznA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7oznM4[M:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7ozoA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozoM4[M:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozpA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozpM4[M:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7pksA5[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7rimA6[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; X-RAY DIFFRACTION 2.9Å

e7oobA1[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7ml0A5[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml1A7[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml2A5[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml4A4[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ripA8[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7riqA3[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7riwA8[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7rixA7[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7riyA1[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7oo3A1[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7oopA7[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7opcA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7opdA9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7meia9[a:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7meiA8[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7mk9A9[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7mkaa8[a:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xn7A3[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xseA1[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xsxA9[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xszA2[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xtdA9[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xt7A2[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xtiA2[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ui9A9[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7uifA3[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7uioAA8[AA:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7uioBA7[BA:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zs9A4[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zsaA3[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zsbA8[A:872-1059] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zwdA9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7zx7A9[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7zx8A2[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8h0vA8[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8h0wA3[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8bvwA6[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8byqA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8bz1A1[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ycx19[1:895-1082] 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

e8p4fA2[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8a40A5[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8b3dA3[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH

; ELECTRON MICROSCOPY

e8oeuA4[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4aA8[A:895-1082] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e7wbvA7[A:873-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

Previous

e4bxxA7[A:872-1059] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

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.

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