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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: Unmapped domains

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

Representatives:

e3hkzC1[C:11-65] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A'' ; X-RAY DIFFRACTION 3.4Å

e4aybC4[C:6-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE ; X-RAY DIFFRACTION 3.20Å

e3hkzM3[M:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A'' ; X-RAY DIFFRACTION 3.4Å

e2pmzC2[C:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A" ; X-RAY DIFFRACTION 3.400Å

e2pmzG2[G:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A" ; X-RAY DIFFRACTION 3.400Å

e4v8sAY4[AY:6-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE SUBUNIT A'' ; X-RAY DIFFRACTION 4.30Å

e4v8sBC3[BC:6-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE SUBUNIT A'' ; X-RAY DIFFRACTION 4.30Å

e2waqC1[C:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT ; X-RAY DIFFRACTION 3.35Å

e2wb1C1[C:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT ; X-RAY DIFFRACTION 3.52Å

e2wb1Y3[Y:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT ; X-RAY DIFFRACTION 3.52Å

e2y0sC3[C:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE SUBUNIT A'' ; X-RAY DIFFRACTION 3.79Å

e2y0sY1[Y:11-65] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE SUBUNIT A'' ; X-RAY DIFFRACTION 3.79Å

e7ok0C4[C:1-61] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A'' ; ELECTRON MICROSCOPY

e7oq4C4[C:1-61] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A'' ; ELECTRON MICROSCOPY

e7oqyC4[C:1-61] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A'' ; ELECTRON MICROSCOPY

e4qiwC2[C:7-59] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit A'' ; X-RAY DIFFRACTION 3.5Å

e5fj8A9[A:920-1084] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC1 ; ELECTRON MICROSCOPY

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