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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

X: cradle loop barrel

Refs: Structure 14, 1489-1498; Current opinion in structural biology 18, 358-365

H: RIFT-related
T: acid protease

126354, 3-crossover-4

T: double psi

152436, 2-crossover-3, 5-crossover-6

F: RNA_pol_Rpb2_6

PF00562 CL0410

Representatives:

e1twfB1[B:814-850,B:975-1097] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE ; ligands: MN,UTP ; X-RAY DIFFRACTION 2.3Å

e1smyC8[C:663-700,C:834-999] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE BETA CHAIN ; ligands: G4P,MG ; X-RAY DIFFRACTION 2.7Å

e4c2mB5[B:762-798,B:912-1040] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 ; X-RAY DIFFRACTION 2.80Å

e5m3fB3[B:762-798,B:912-1040] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase I subunit RPA135 ; ELECTRON MICROSCOPY

e5m3mB7[B:762-798,B:912-1040] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase I subunit RPA135 ; ELECTRON MICROSCOPY

e7okxB2[B:845-882,B:1007-1132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ok0B2[B:710-747,B:871-996] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit B ; ELECTRON MICROSCOPY

e6rflB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-dependent RNA polymerase subunit rpo132 ; ELECTRON MICROSCOPY

e6ricB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-dependent RNA polymerase subunit rpo132 ; ELECTRON MICROSCOPY

e6ridB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-dependent RNA polymerase subunit rpo132 ; ELECTRON MICROSCOPY

e6rieB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-dependent RNA polymerase subunit rpo132 ; ELECTRON MICROSCOPY

e7okyB2[B:845-882,B:1007-1132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ol0B2[B:845-882,B:1007-1132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oq4B2[B:710-747,B:871-996] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit B ; ELECTRON MICROSCOPY

e7oqyB2[B:710-747,B:871-996] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit B ; ELECTRON MICROSCOPY

e7amvB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase ; ELECTRON MICROSCOPY

e7aofB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase ; ELECTRON MICROSCOPY

e7aohB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase ; ELECTRON MICROSCOPY

e7aozB2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase ; ELECTRON MICROSCOPY

e7ap8B2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase ; ELECTRON MICROSCOPY

e7ap9B2[B:733-769,B:878-1022] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase ; ELECTRON MICROSCOPY

e7eu0B2[B:762-799,B:909-1044] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerases IV and V subunit 2 ; ELECTRON MICROSCOPY

e7eu1B2[B:762-799,B:909-1044] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerases IV and V subunit 2 ; ELECTRON MICROSCOPY

e7fjiB2[B:729-766,B:892-1016] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase III subunit RPC2 ; ELECTRON MICROSCOPY

e7fjjB2[B:729-766,B:892-1016] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase III subunit RPC2 ; ELECTRON MICROSCOPY

e7oo3B2[B:768-805,B:930-1055] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oobB2[B:768-805,B:930-1055] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oopB2[B:768-805,B:930-1055] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7opcB2[B:768-805,B:930-1055] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7opdB2[B:768-805,B:930-1055] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oznB2[B:769-805,B:930-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oznN2[N:769-805,N:930-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozoB2[B:769-805,B:930-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozoN2[N:769-805,N:930-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozpB2[B:769-805,B:930-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozpN2[N:769-805,N:930-1061] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7pksB2[B:768-805,B:930-1055] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e4by7B5[B:814-850,B:975-1097] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 ; X-RAY DIFFRACTION 3.15Å

e2e2iB8[B:814-850,B:975-1097] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE ; ligands: DGT ; X-RAY DIFFRACTION 3.41Å

e4kmuC7[C:791-827,C:1063-1239] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA ; X-RAY DIFFRACTION 3.85Å

e4s20C1[C:791-828,C:1060-1237] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; X-RAY DIFFRACTION 4.7Å

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.

T: AbrB

122'1'344'3', 2-crossover-3, 2'-crossover-3'

T: Bacterial fluorinating enzyme-C

1265437, 2-crossover-3, 6-crossover-7

T: FMN-binding split barrel

123654, 3-crossover-4

T: Surface presentation of antigens (SPOA)

123654, 3-crossover-4, swapping

T: Alanine racemase-C

125436, 2-crossover-3, 5-crossover-6

T: Aminomethyltransferase beta-barrel domain

143256, 1-crossover-2, 4-crossover-5

T: PUA domain

12543, 2-crossover-3

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

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