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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: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
F: RNA_pol_Rpb1_7

PF04990

Representatives:

e1twfA3[A:1142-1272] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7egao8[o:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7egbo4[o:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7nvrA9[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7nvsA2[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvtA4[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvuA5[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvyA4[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nvzA7[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7nw0A9[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e6xreA4[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7kedA1[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7o4iA2[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7egco5[o:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7b7uA4[A:1152-1308] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7nkyA3[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7keeA3[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7kefA7[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7o4jA1[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7o72A6[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7o73A5[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7o75A9[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7f4gA6[A:1163-1299] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7okxA7[A:1165-1298] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7nkxA7[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e6gmhA7[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7okyA7[A:1165-1298] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7ol0A7[A:1164-1299] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7oznA6[A:1165-1298] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7oznM6[M:1165-1298] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RPB1 ; ELECTRON MICROSCOPY

e7ozoA6[A:1165-1298] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozoM6[M:1165-1298] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozpA6[A:1165-1296] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ozpM6[M:1165-1296] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7pksA7[A:1164-1299] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7rimA3[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7oobA7[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7ml0A3[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml1A4[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml2A4[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ml4A1[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ripA2[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7riqA7[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7riwA5[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7rixA3[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7riyA8[A:1142-1272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e7oo3A4[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7oopA6[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7opcA6[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7opdA1[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7meia5[a:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7meiA7[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7mk9A1[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7mkaa3[a:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xn7A9[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xseA3[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xsxA2[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xszA4[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xtdA1[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xt7A1[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7xtiA1[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ui9A5[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7uifA1[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7uioAA3[AA:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7uioBA5[BA:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zs9A6[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zsaA2[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zsbA2[A:1132-1242] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB1 ; ELECTRON MICROSCOPY

e7zwdA7[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7zx7A2[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7zx8A1[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8h0vA3[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8h0wA2[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8bvwA7[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8byqA6[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e8bz1A3[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit ; ELECTRON MICROSCOPY

e7ycx18[1:1165-1297] 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

e8p4fA1[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8a40A9[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8b3dA8[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH

; ELECTRON MICROSCOPY

e8oeuA9[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e8p4aA1[A:1165-1297] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

e7wbvA4[A:1134-1244] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ELECTRON MICROSCOPY

Previous
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