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

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

X: Transducin (heterotrimeric G protein), gamma chain

X: Anti-sigma factor FlgM

X: Epsilon subunit of mitochondrial F1F0-ATP synthase

X: RNA polymerase sigma-54 factor N-terminal region

X: Ezh2 N-terminal domain

X: Pre-mRNA-splicing helicase BRR2 NC-clamp

X: Alpha-crystallin B chain N-terminal domain

X: Pre-mRNA-processing factor 31 C-terminal region

X: U4/U6 small nuclear ribonucleoprotein PRP3 N-terminal region

X: Baseplate wedge protein gp7 domain VI

X: Herpes DNA polymerase N-terminal domain

X: Copper resistance protein ScsC N-terminal region

X: Cell division factor MciZ

X: Proteinase A inhibitor IA3

X: Glu-tRNAGln amidotransferase C subunit

X: RelB-like

X: Intraflagellar transport protein 46 C-terminal domain

X: Intraflagellar transport protein 52 C-terminal domain

X: Exosome complex exonuclease RRP6 N-terminal domain

X: Exosome complex protein LRP1

X: Anti sigma factor NepR-related

X: Lag-3 N-terminal region

X: Adhesin P1 N-terminal domain

X: Fe-only hydrogenase smaller subunit

X: Methanol dehydrogenase subunit

X: Moesin tail domain

X: Ribosomal protein L39e

X: Mitoribosomal protein mS26

X: Mitoribosomal protein mS31

X: Mitoribosomal protein mS33

X: Mitoribosomal protein mS38

X: Mitoribosomal protein mL42

X: Mitoribosomal protein mL52

X: Mitoribosomal protein mL63

X: C-terminal helical region in 60S ribosomal protein L4 (L4p)

X: Ribosomal protein L41-A

X: NC100

X: Stathmin

X: Clathrin light chain B

X: N-terminal domain of bifunctional PutA protein

X: Stage V sporulation protein M

X: YgaP transmembrane domain

X: Nicastrin transmembrane helix

X: Photosystem II reaction centre subunit H, transmembrane region

X: Bd-type quinol oxidase transmembrane helix subunit

X: Mitochondrial complex I, B9 subunit

X: Mitochondrial complex I, AGGG subunit

X: Mitochondrial complex I, KFYI subunit

X: Mitochondrial complex I, MNLL subunit

X: Mitochondrial complex I, MWFE subunit

X: Mitochondrial complex I, SGDH subunit

X: Mitochondrial complex I, B14.5b subunit

X: Mitochondrial complex I, B16.6 subunit

X: CAA3-type cytochrome c oxidase subunit IV

X: Mitochondrial cytochrome c oxidase subunit IV

X: Mitochondrial cytochrome c oxidase subunit VIa

X: Mitochondrial cytochrome c oxidase subunit VIc

X: Mitochondrial cytochrome c oxidase subunit VIIa

X: Mitochondrial cytochrome c oxidase subunit VIIb

X: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)

X: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)

X: Bacterial aa3 type cytochrome c oxidase subunit IV

X: Bacterial ba3 type cytochrome c oxidase subunit IIa

X: cytochrome c1 transmembrane anchor

X: iron-sulfur subunit (ISP) transmembrane anchor

X: Multidrug efflux pump accessory protein AcrZ

X: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor

X: PetG subunit of the cytochrome b6f complex

X: PetL subunit of the cytochrome b6f complex

X: PetM subunit of the cytochrome b6f complex

X: PetN subunit of the cytochrome b6f complex

X: Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

X: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

X: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

X: Subunit III of photosystem I reaction centre, PsaF

X: Subunit VIII of photosystem I reaction centre, PsaI

X: Subunit IX of photosystem I reaction centre, PsaJ

X: Subunit XII of photosystem I reaction centre, PsaM

X: Subunit PsaX of photosystem I reaction centre

X: Subunit VI of Photosystem I reaction centre

X: Subunit N of Photosystem I reaction centre

X: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor

X: Preprotein translocase SecE subunit

X: Sec-beta subunit

X: Oligosaccharyltransferase subunit ost4p

X: Photosystem II reaction center protein L, PsbL

X: Photosystem II reaction center protein J, PsbJ

X: Photosystem II 10 kDa phosphoprotein PsbH

X: Photosystem II reaction center protein T, PsbT

X: Photosystem II reaction center protein M, PsbM

X: Photosystem II reaction center protein K, PsbK

X: Photosystem II reaction center protein I, PsbI

X: Photosystem II reaction center protein ycf12

X: Photosystem II reaction center W protein, chloroplastic

X: Photosystem II PsbX protein

X: Photosystem II protein Y, psbY

X: Chlorosome Protein A

X: Cytochrome b559 subunits

X: Cytochrome c oxidase subunit II-like, transmembrane region

X: Glycophorin-A transmembrane domain

X: NADH-quinone oxidoreductase subunit A

X: NADH-quinone oxidoreductase subunit J

X: Agnoprotein

X: Viral membrane protein P3

X: Viral membrane protein P6

X: Transmembrane protein 141

X: Transmembrane protein 14A

X: HIG1 domain family member 1A

X: Interferon alpha-inducible protein 27-like protein 1

X: Intrinsic membrane protein pufX

X: F1F0 ATP synthase subunit C

X: Magnesium transport protein CorA, transmembrane region

X: Sensor proteins transmembrane domains

X: PsbZ-like

X: F-type ATP synthase subunit b

X: ATP synthase D chain-like

X: Mitochondrial ATP synthase coupling factor 6

X: Small-conductance potassium channel

X: Gated mechanosensitive channel

X: Bacterial light-harvesting complex subunits

X: Chlorophyll a-b binding protein

X: Transmembrane helices in MalF N-terminal region

X: Transmembrane helix in sodium-potassium ATPase beta subunit

X: Twin-arginine transport (Tat) system component TatA

X: Histidine kinase receptor ArcB membrane domain

X: Histidine kinase receptor QseC membrane domain

X: MerF

X: Fibroblast growth factor receptor 3 transmembrane domain

X: Epidermal growth factor receptor transmembrane-juxtamembrane segment-like

X: Transmembrane segment of lysosome-associated membrane glycoprotein 2

X: Notch transmembrane helix

X: AF1503 pre-HAMP domain

X: Envelope small membrane protein

X: C-terminal domain of VP7

X: Connexin43

X: iron-sulfur center-binding helical hairpin

X: 50S ribosomal protein L34

X: RNA polymerase PB1 C-terminal fragment

X: RNA polymerase PB2 N-terminal fragment

X: inhibitory phosphorylation domain of myosin phosphatase targeting subunit 1

X: E-cadherin

X: Synaptobrevin

X: Gle2-binding sequence (GLEBS) of Nup98

X: HIV-1 Tat

X: N-terminal domain of RFX5

X: Regulatory factor X-associated protein C-terminal domain

X: p53 transactivation domain

X: 40S ribosomal protein S30 (S30e)

X: Telomere length regulator taz1

X: small heat shock protein (Hsp12)

X: RPEL domain

X: Mediator of RNA polymerase II transcription subunit 6

X: N-terminal regulatory segment of carnitine palmitoyltransferase 1A

X: RPL13

X: RPL29

X: E3 SUMO-protein ligase RanBP2 fragment

X: Wiskott-Aldrich syndrome protein family member 1

X: Alpha-synuclein

X: Chaotic nuclear migration protein 67

X: N-terminal region in 40S ribosomal protein rpS2 (S5p)

X: Helical hairpin in Ndc80

X: Phoptry protein fragment

X: IBB domain

X: Helical arch in Ski2-like helicases

X: regulatory domain of a plasma-membrane Ca2+-ATPase

X: DCP1-binding motif

X: Suppressor protein STM1

X: Holliday junction recognition protein N-terminal domain

X: Ubiquitin-binding motif (UBM)

X: Glycyl radical domain

X: ExsE

X: mRNA-decapping enzyme 1A trimerization domain

X: Apolipoprotein C-III

X: Major vault protein (MVP) helical domain

X: Small envelope protein M

X: uncharacterized protein RhR2

X: Splicing factor 1 N-terminal domain

X: Helical linker in baseplate protein ORF48

X: Methanogenic A1A0 ATP synthase stalk subunit H dimerization domain

X: UIM domain

X: Integrin beta-1D cytoplasmic tail

X: 30S ribosomal protein S21

X: FATC domain

X: Translation machinery-associated protein 46 DFRP domain

X: Voltage gated calcium channel IQ domain

X: Fusion glycoprotein F2

X: NHR2 domain-like

X: Transmembrane helix of outer membrane lipoprotein Wza

X: Apolipoprotein A-II

X: FXYD family

X: Toxofilin

X: Preprotein translocase subunit YajC

X: Transmembrane helix of nickel-iron hydrogenase small subunit

X: Transmembrane helix of E1 envelope glycoprotein

X: N-terminal domain of small heat shock protein Tsp36

X: N-terminal region of NMB0537

X: Ubc7p-binding domain of Cue1p

X: Phycoerythrin 545 alpha-subunits

X: Ubiquinol-cytochrome c reductase 8 kDa protein

X: Virulence effector SptP domain

X: Outer membrane virulence protein yopE

X: TSP9-like

X: C-terminal region of nonsense mediated decay factor UPF2

X: C-terminal region of sodium/hydrogen exchange regulatory factor 1

X: Stage II sporulation protein SB

X: TraN protein

X: Colicin S4 translocation domain

X: Cytoplasmic domain of CD3 epsilon chain

X: cGMP phosphodiesterase gamma subunit

X: Immunodominant antigen Pgp3 helical domain

X: Helical region in REST corepressor 1

X: Helical region in V-type proton ATPase subunit E

X: V-type proton ATPase subunit G

X: Myeloma immunoglobulin D delta linker region

X: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain

H: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain

T: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain

F: CSN5_C

PF18323

Representatives:

e4d10E2[E:251-333] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 SIGNALOSOME COMPLEX SUBUNIT 5 ; X-RAY DIFFRACTION 3.80Å

e8h3aE1[E:251-332] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

e8h3fE2[E:251-332] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

e4wsnM2[M:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; X-RAY DIFFRACTION 5.500Å

e4wsnU2[U:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; X-RAY DIFFRACTION 5.500Å

e4wsnc1[c:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; X-RAY DIFFRACTION 5.500Å

e4wsnk2[k:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; X-RAY DIFFRACTION 5.500Å

e4wsns1[s:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; X-RAY DIFFRACTION 5.500Å

e4d10M1[M:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 SIGNALOSOME COMPLEX SUBUNIT 5 ; X-RAY DIFFRACTION 3.80Å

e4d18E1[E:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 SIGNALOSOME COMPLEX SUBUNIT 5 ; X-RAY DIFFRACTION 4.08Å

e4d18M1[M:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 SIGNALOSOME COMPLEX SUBUNIT 5 ; X-RAY DIFFRACTION 4.08Å

e4wsnE1[E:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; X-RAY DIFFRACTION 5.500Å

e6r6hE2[E:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

e6r7fE2[E:251-334] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

e6r7hE1[E:251-334] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

e6r7iE2[E:251-333] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

e8h38E1[E:251-332] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COP9 signalosome complex subunit 5 ; ELECTRON MICROSCOPY

F: MitMem_reg

PF13012

F: eIF3h_C

PF19445

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: 26S proteasome regulatory subunits C-terminal helices

X: Antiviral helicase Ski2 N-terminal extended region

X: Norovirus NS1/2 N-terminal domain

X: ParE2-associated antitoxin 2 (PaaA2)

X: Mitochondrial 54S ribosomal protein L28

X: Mitochondrial 54S ribosomal protein L27

X: Mitochondrial 54S ribosomal protein L25

X: Mitochondrial 54S ribosomal protein L31

X: Nup54 C-terminal interacting domain

X: Toll-like receptor 3 transmembrane domain

X: CRY-binding domain of PER

X: 4E-BP2

X: Transmembrane helix of sigma-1 receptor

X: mitochondrial aminolevulinate synthase C-terminal domain

X: TOR1 N-terminal extended segment

X: Palmitoyltransferase DHHC C-terminal domain

X: C-terminal portion of ANKRD31

X: Prp8-binding region of SLU7

special