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

X: N-terminal domain of TAP-binding protein-related

X: P22 coat protein insertion domain

X: Catalytic domain of hepatitis C virus NS2-3 protease

X: N-terminal domain of minor coat protein pIII

X: uncharacterized protein RUMGNA_01417

X: Ribosomal protein L21p

X: Ribosomal protein L25-like

X: Uncharacterized protein from gene locus rrnAC0354

X: Replication foci-targeting sequence N-terminal domain

X: Protein CLP1 C-terminal domain

X: Glycoside hydrolase family 127 C-terminal domain

X: EV matrix protein

X: LigT-like

X: Urease metallochperone UreE-N

X: Target recognition domain of zoocin A

X: Polymyxin B resistance protein

X: Cuben fold of PcncAAAD

X: OB-fold

X: GroES-like

X: Uncharacterized protein Dsy0195

X: SH3

X: IL8-related

X: UL131A-like

X: UL128 C-terminal domain

X: Cell division protein ZapC N-terminal domain

X: hypothetical protein TTMA177

X: Hantavirus structural glycoprotein Gn ectodomain subdomain III

X: MutM N-terminal domain-like

X: Ribosomal protein L14-like

X: YopX, C-terminal domain-like

X: VC0467-like

X: MMP1218-like

X: MFPT repeat

X: Barrel domain in upper collar protein

X: barrel domain in putative modulator of DNA gyrase, PmbA/TldD

X: beta-barrel domain in acetyl-CoA synthetase-like proteins

X: FimD N-terminal domain-like

X: Micronemal adhesive repeat

X: Coronavirus NSP8-like

X: PDZ domain

X: all-beta domain in DNA topoisomerase IV alpha subunit

X: hypothetical protein PA3229

X: beta-clip

X: Cyclophilin-like

X: SPOC domain-like

X: Herpes virus serine proteinase, assemblin

X: Oncogene product-like

X: Mannose 6-phosphate receptor domain

X: FMT C-terminal domain-like

X: Sortase

X: XRCC4, N-terminal domain-like

X: Virulence associated protein B (Vapb)

X: BH3618-like

X: GspC HR domain/PilP-like

X: CRISPR-Cas effector Cas13d N-terminal domain

X: Lipocalins/Streptavidin

X: YmcC-like

X: Lysosome membrane protein 2 lumenal domain

X: Handle domain in transferrin-binding protein B

X: Rubella virus capsid protein C-terminal domain

X: Single-stranded DNA-binding protein DdrB

X: Allergen Alt a 1

X: FomD-like

X: Outer membrane meander beta-barrels

X: secretin domain

X: Factor H-binding protein (fHbp) N-terminal beta-barrel domain

X: STT3/PglB/AglB beta-barrel domain

X: Acetoacetate decarboxylase-like

X: AttH-like

X: Barrel domain in heme-dependent catalases

X: WWE domain

X: GFP-like

X: Transcriptional factor tubby, C-terminal domain

X: Oxysterol-binding protein

X: CBF-like

X: NifT/FixU

X: barrel domain in CV3147-like proteins

X: Pfam PF06938 (DUF1285)

X: PH domain-like

H: PH domain-like

T: PH domain-like

F: Sharpin_PH

F: FERM_C_FAK1

F: BBL5

F: bPH_1

F: DCP1

F: PH_13

F: GRAM

F: PID,DAB2_SBM

F: PH_14

F: PH_9

F: PID

F: PH_12

F: IQ_SEC7_PH

F: PH_18

F: SYCP2_SLD

F: Carm_PH

F: IRS

F: POB3_N

F: DAB2_SBM

F: PH_20

F: ISP3_C

F: PH_RBD

F: PH-GRAM_MTMR6-like

F: SPT16

F: FERM_C1_MyoVII

F: SCAB-PH

F: APP_amyloid

F: REC114-like

F: Sec3-PIP2_bind

F: SSrecog

F: PH_NF1

F: PH_8

F: Rttp106-like_middle

F: PH_16

F: PH

F: WH1,Retinal

F: UCH_N

F: SOS1_NGEF_PH

F: PH_TFIIH

F: ZFYVE21_C

F: Jak1_Phl

F: hSac2

F: PH_17

F: Voldacs

F: ISP1_C

F: FERM_C

F: Rpn13_ADRM1_Pru

Representatives:

e2kr0A1[A:1-132] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; SOLUTION NMR

e4b4tX1[X:7-132] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e2r2yA1[A:22-130] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein ADRM1 ; X-RAY DIFFRACTION 1.67Å

e2z59A1[A:22-130] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein ADRM1 ; SOLUTION NMR

e2z4dA1[A:6-101] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; SOLUTION NMR

e4c0vX1[X:7-134] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4cr2X1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S PROTEASOME REGULATORY SUBUNIT RPN13 ; ELECTRON MICROSCOPY

e4cr3X1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S PROTEASOME REGULATORY SUBUNIT RPN13 ; ELECTRON MICROSCOPY

e4cr4X1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S PROTEASOME REGULATORY SUBUNIT RPN13 ; ELECTRON MICROSCOPY

e5a5bX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S PROTEASOME REGULATORY SUBUNIT RPN13 ; ELECTRON MICROSCOPY

e3jcoX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e3jcpX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e2nbvA1[A:21-130] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; SOLUTION NMR

e5irsA1[A:21-130] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; ligands: DTT ; X-RAY DIFFRACTION 1.796Å

e5mpdX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5mpeX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5mpbX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5mpcX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5wviX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5wvkX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5v1yA1[A:18-131] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; X-RAY DIFFRACTION 1.42Å

e5v1yB1[B:20-132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; X-RAY DIFFRACTION 1.42Å

e5v1zA1[A:20-131] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; X-RAY DIFFRACTION 2.00Å

e5v1zB1[B:21-132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; X-RAY DIFFRACTION 2.00Å

e2nbkA1[A:20-130] Image Pymol Jmol Links: PDB, SCOP, CATH

e6co4A1[A:20-132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; SOLUTION NMR

e6fvtX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6fvwX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6fvuX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6fvvX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6fvxX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6fvyX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6j2cX1[X:7-117] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6j2xX1[X:7-117] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6j2qX1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e5ymyC1[C:19-132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; SOLUTION NMR

e6j2nX1[X:7-117] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6j30X1[X:7-117] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e6oi4A1[A:20-131] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; ligands: EDO ; X-RAY DIFFRACTION 1.76Å

e6oi4B1[B:21-131] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; ligands: EDO ; X-RAY DIFFRACTION 1.76Å

e6uyiA1[A:20-132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; SOLUTION NMR

e6uyjA1[A:20-132] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; SOLUTION NMR

e7kxiA1[A:21-130] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Proteasomal ubiquitin receptor ADRM1 ; ligands: XAY ; SOLUTION NMR

e7qo5X1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e7qo3X1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

26S proteasome regulatory subunit RPN13 ; ELECTRON MICROSCOPY

e7qo6X1[X:7-133] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HLJ1_G0030700.mRNA.1.CDS.1 ; ELECTRON MICROSCOPY

F: Myosin_TH1

F: PH_Tiam1

F: PH_3

F: SIN1_PH

F: ASK_PH

F: ECT2_PH

F: SNX17_FERM_C

F: INPP5B_PH

F: CARM1

F: DUF1681

F: PH1_SSRP1-like

F: OCRL_clath_bd

F: PH_BEACH

F: ICAP-1_inte_bdg

F: PTB

F: DM10_dom

F: EhRGS-RhoGEF_PH-like

F: EVH1_PP4R3

F: WH1

F: Ran_BP1

F: Vps36_ESCRT-II

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.

H: PA2021-like

H: first barrel domain in viral glycoproteins

H: second barrel domain in viral glycoproteins

H: NucS N-terminal domain

H: Uncharacterized protein PA3793

X: Internal protein I

X: LARA domain

X: Restriction endonuclease PabI

X: N-terminal domain in DUF2118 family

X: Pestivirus Npro endopeptidase C53

X: Repulsive guidance molecule (RGM) family

X: V1/V2 domain in HIV gp120

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

special