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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: alpha/beta-Hammerhead/Barrel-sandwich hybrid
H: alpha/beta-Hammerhead/Barrel-sandwich hybrid
T: Single hybrid motif
F: RNA_pol_Rpb2_6

PF00562 CL0410

Representatives:

e1twfB3[B:851-974] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE ; X-RAY DIFFRACTION 2.3Å

e1smyC9[C:701-833] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4c2mB6[B:799-911] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4by7B6[B:851-974] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e5ip7B1[B:851-974] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB2 ; X-RAY DIFFRACTION 3.520Å

e5ip9B7[B:851-974] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB2 ; X-RAY DIFFRACTION 3.450Å

e2e2hB5[B:851-974] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE ; X-RAY DIFFRACTION 3.95Å

e2nvzB5[B:851-974] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II 140 kDa polypeptide ; X-RAY DIFFRACTION 4.2Å

e2pmzB6[B:750-872] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e2pmzR7[R:750-872] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4b1oB7[B:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4aybB4[B:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE ; ligands: ZN ; X-RAY DIFFRACTION 3.20Å

e3hkzJ3[J:750-872] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e3hkzB1[B:750-872] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4v8sAR1[AR:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE ; X-RAY DIFFRACTION 4.30Å

e4v8sBB2[BB:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE ; X-RAY DIFFRACTION 4.30Å

e4b1pR7[R:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e3h0gN2[N:840-963] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB2 ; X-RAY DIFFRACTION 3.650Å

e3h0gB5[B:840-963] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase II subunit RPB2 ; X-RAY DIFFRACTION 3.650Å

e2y0sB5[B:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE ; X-RAY DIFFRACTION 3.79Å

e2wb1R7[R:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT ; X-RAY DIFFRACTION 3.52Å

e2wb1B2[B:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT ; X-RAY DIFFRACTION 3.52Å

e2waqB5[B:753-875] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT ; X-RAY DIFFRACTION 3.35Å

e7okxB7[B:883-1006] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ok0B7[B:748-870] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit B ; ELECTRON MICROSCOPY

e7okyB7[B:883-1006] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ol0B7[B:883-1006] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oq4B7[B:748-870] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit B ; ELECTRON MICROSCOPY

e7fjiB7[B:767-891] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase III subunit RPC2 ; ELECTRON MICROSCOPY

e7oo3B7[B:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7opdB7[B:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oznB6[B:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7oznN6[N:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozoB6[B:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozoN6[N:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7ozpB6[B:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e7pksB7[B:806-929] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA-directed RNA polymerase subunit beta ; ELECTRON MICROSCOPY

e2e2iB9[B:851-974] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4kmuC5[C:713-790] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4kmuC6[C:828-938,C:1045-1062] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4s20C5[C:829-977,C:1011-1059] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

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

e4s20C7[C:714-790] 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.

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