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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: LuxS, MPP, ThrRS/AlaRS common domain

looks like an elaborated ferredoxin

X: ClpS-like

contains a HTH motif

X: Ribosomal protein S5 domain 2-like
H: Ribosomal protein S5 domain 2-like
T: Ribosomal protein S5 domain 2-like
F: RNase_PH

PF01138 CL0329

Representatives:

e2je6A2[A:1-191] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 2 ; ligands: 1PE,PEG ; X-RAY DIFFRACTION 1.6Å

e2je6B2[B:8-155] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 1.6Å

e4ifdF1[F:4-22,F:42-185] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Exosome complex component MTR3 ; ligands: BR ; X-RAY DIFFRACTION 2.805Å

e2jebB2[B:9-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.4Å

e2c38B2[B:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2br2B2[B:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c38J2[J:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2c37V2[V:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,NA,U5P ; X-RAY DIFFRACTION 2.8Å

e2br2H2[H:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c38D2[D:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 3.1Å

e2br2X2[X:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c37D2[D:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c38X2[X:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2c39P2[P:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c39X2[X:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c38V2[V:9-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2nn6B2[B:6-150] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP41 ; X-RAY DIFFRACTION 3.35Å

e2c39R2[R:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c37F2[F:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,U5P ; X-RAY DIFFRACTION 2.8Å

e2br2T2[T:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c39T2[T:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c39D2[D:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c37R2[R:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c39V2[V:9-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c37N2[N:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,RP5,U5P ; X-RAY DIFFRACTION 2.8Å

e2br2N2[N:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c37H2[H:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,U5P ; X-RAY DIFFRACTION 2.8Å

e2ba1D2[D:10-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Archaeal exosome complex exonuclease RRP41 ; X-RAY DIFFRACTION 2.7Å

e2c37P2[P:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c37B2[B:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,U5P ; X-RAY DIFFRACTION 2.8Å

e2c38H2[H:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2ba0F2[F:10-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Archaeal exosome RNA binding protein RRP41 ; X-RAY DIFFRACTION 2.7Å

e2c38N2[N:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2c39B2[B:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2ba0D2[D:10-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Archaeal exosome RNA binding protein RRP41 ; X-RAY DIFFRACTION 2.7Å

e2c39J2[J:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2br2V2[V:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c39L2[L:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2c39F2[F:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2br2R2[R:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c38P2[P:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 3.1Å

e2ba1F2[F:10-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Archaeal exosome complex exonuclease RRP41 ; X-RAY DIFFRACTION 2.7Å

e2c37T2[T:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c38T2[T:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 3.1Å

e2c38R2[R:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 3.1Å

e2br2P2[P:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c38L2[L:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 3.1Å

e2br2J2[J:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2br2D2[D:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c39N2[N:10-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2jeaB2[B:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; X-RAY DIFFRACTION 2.33Å

e2c37L2[L:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2c37J2[J:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,U5P ; X-RAY DIFFRACTION 2.8Å

e2c38F2[F:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: AMP,CL ; X-RAY DIFFRACTION 3.1Å

e2ba0E2[E:10-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Archaeal exosome RNA binding protein RRP41 ; X-RAY DIFFRACTION 2.7Å

e2c37X2[X:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL,U5P ; X-RAY DIFFRACTION 2.8Å

e2br2F2[F:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2ba1E2[E:10-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Archaeal exosome complex exonuclease RRP41 ; X-RAY DIFFRACTION 2.7Å

e2br2L2[L:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CL ; X-RAY DIFFRACTION 2.8Å

e2wnrB2[B:15-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: PO4 ; X-RAY DIFFRACTION 2.65Å

e3m7nD2[D:8-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; X-RAY DIFFRACTION 2.4Å

e3l7zB2[B:7-152] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.41Å

e4ba1B2[B:-1-146] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: NA,PO4 ; X-RAY DIFFRACTION 1.8Å

e2pnzA2[A:9-151] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: 5GP,MPD,UDP ; X-RAY DIFFRACTION 2.14Å

e2c39H2[H:17-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 3.3Å

e2po0A2[A:9-151] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: ADP ; X-RAY DIFFRACTION 2.3Å

e2po1A2[A:9-151] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: MPD ; X-RAY DIFFRACTION 1.94Å

e2po2A2[A:9-151] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: CDP,MPD ; X-RAY DIFFRACTION 2.41Å

e3l7zH2[H:5-152] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.41Å

e3m7nE2[E:6-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; X-RAY DIFFRACTION 2.4Å

e3m7nF2[F:8-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; X-RAY DIFFRACTION 2.4Å

e3m85E2[E:6-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; X-RAY DIFFRACTION 3.0Å

e3m85F2[F:8-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; X-RAY DIFFRACTION 3.0Å

e3l7zE2[E:2-152] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; ligands: SO4 ; X-RAY DIFFRACTION 2.41Å

e2wnrF2[F:14-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: PO4 ; X-RAY DIFFRACTION 2.65Å

e3m85D2[D:8-153] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable exosome complex exonuclease 1 ; X-RAY DIFFRACTION 3.0Å

e2wnrD4[D:16-152] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: PO4 ; X-RAY DIFFRACTION 2.65Å

e3krnA4[A:3-115] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN C14A4.5, CONFIRMED BY TRANSCRIPT EVIDENCE ; X-RAY DIFFRACTION 3.92Å

e3krnB3[B:2-35,B:60-121] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN C14A4.5, CONFIRMED BY TRANSCRIPT EVIDENCE ; X-RAY DIFFRACTION 3.92Å

e4ba2B3[B:8-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 ; ligands: NA,PO4 ; X-RAY DIFFRACTION 2.5Å

e1r6lA2[A:1-151] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBONUCLEASE PH ; ligands: NHE,SO4 ; X-RAY DIFFRACTION 1.9Å

e1e3hA5[A:3-151] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GUANOSINE PENTAPHOSPHATE SYNTHETASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.600Å

e1e3hA6[A:346-482] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GUANOSINE PENTAPHOSPHATE SYNTHETASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.600Å

e5k36C1[C:10-286] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Exosome complex component RRP43 ; ligands: SO4 ; X-RAY DIFFRACTION 3.100Å

e2nn6A2[A:1-184] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYMYOSITIS/SCLERODERMA AUTOANTIGEN 1 ; X-RAY DIFFRACTION 3.35Å

e2nn6C2[C:7-187] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP43 ; X-RAY DIFFRACTION 3.35Å

e2nn6D2[D:25-146] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP46 ; X-RAY DIFFRACTION 3.35Å

e2nn6E2[E:5-191] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPLEX EXONUCLEASE RRP42 ; X-RAY DIFFRACTION 3.35Å

e2nn6F2[F:29-72,F:92-175] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EXOSOME COMPONENT 6 ; X-RAY DIFFRACTION 3.35Å

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 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