3D Domain Swap Systems - ProSwap

3D domain-swapped systems are characterized by the interconversion between ‘closed’ monomeric proteins and an intertwined homo-oligomer, where specific intramolecular contacts are substituted for their intermolecular equivalents (Bennett et al., 1994; Bennett et al., 1995; Liu and Eisenberg, 2002). These systems involve the exchange of structural domains as well as chain segments that do not correspond to such domains.

Here we list 115 3D domain-swapped systems identified from the PDB (January 2011 snapshot) using automatic procedures. These procedures identify pairs of monomer and homo-oligomers with the same or related sequences, where the non-contiguous structural domain in the oligomer is similar enough to the structure of the monomer (see MacKinnon et al. 2012).

In some cases, such as RNase A, multiple 3D domains swapped systems are reported for the same protein family. In rare cases, such as the prion protein, two separate entries are provided for seemingly similar swaps, because the protein sequences in these entries differ significantly in length, which resulted in assigning them to distinct sequence families.

System	Name	Representative Interface	# of Swapped Residues	RIAD	Symmetry
79	Human hPDE2A catalytic domain	3itu-1	13	0.819	Dimeric
115	Tudor domain of human JMJD2C	2xdp-1	15	0.661	Dimeric
101	Mammalian actin bundling protein Iba1/2	1wy9-1	16	0.398	Dimeric
29	Mammalian retromer complex protein Vps29	3psn-1	13	0.598	Dimeric
102	Prokaryotic dissimilatory sulfite reductase I/II	3mma-5	15	0.310	Dimeric
74	Thermophilic bacterial ribosomal protein S15	1a32-1	14	0.702	Polymeric
80	Bacterial protein L	1k50-1	11	0.867	Dimeric
90	Protease inbibitor ecotin	1slv-1	12	0.613	Dimeric
27	SRCR domain of mouse MARCO	2oya-1	13	0.811	Dimeric
71	Bacterial phosphocarrier protein N-terminus Swap	2ak7-1	12	0.839	Dimeric
38	Variable fragment domain of mammalian antibody	1sjv-1	15	0.876	Polymeric
69	Mammalian prion protein	3haf-1	34	0.764	Dimeric
66	C-terminal peptidoglycan-binding domain of human peptidoglycan recognition proteins	1sk4-1	22	0.692	Dimeric
43	Alicyclobacillus acidocaldarius thermophilic esterase EST2	1u4n-1	37	0.498	Dimeric
14	Shigella flexneri signaling protein IpgB2	3lyq-1	31	0.767	Dimeric
83	Human interleukin-10	1inr-1	43	0.933	Dimeric
107	Helicobacter pylori ISHp608 transposase	2a6m-2	9	0.884	Dimeric
16	Pyrococcus horikoshii Ph1109	2e6u-1	7	0.468	Dimeric
63	HIV-1 envelope protein gp41	1dlb-1	29	0.099	Oligomeric
58	Escherichia coli DraE adhesin	1ut1-3	11	0.337	Oligomeric
72	Bacillus subtilis probable glutaminase APC1040	2osu-2	8	0.741	Polymeric
17	Escherichia coli cell adhesion protein FaeG	2j6g-1	12	0.688	Dimeric
110	Bovine calbindin D9k	1ht9-1	32	0.793	Dimeric
78	Mammalian receptor protein tyrosine phosphatase	3b7o-1	18	0.624	Dimeric
5	RING finger domain	3ng2-1	9	0.826	Dimeric
54	Bacteriophage T4 GP9	1qex-3	15	0.764	Dimeric
1	Ligand-binding domain of mammalian estrogen-related receptor gamma	1s9q-2	10	0.496	Dimeric
51	Bacterial thioredoxin	3die-1	30	0.862	Dimeric
19	Cytochrome C Dimeric Swap	3nbs-1	23	0.866	Dimeric
84	SH2 domain of human Grb14	2qms-2	9	0.466	Dimeric
73	Mammalian importin	2jdq-1	16	0.716	Dimeric
99	Chlamydomonas reinhardtii homing endonuclease I-CreI	2o7m-1	13	0.502	Dimeric
87	Human IGF-1R kinase	3d94-1	10	0.471	Dimeric
47	Mammalian class I histocompatibility antigen/?2 microglobulin	3low-1	39	0.972	Dimeric
76	Proteobacterial hemophore	2cn4-1	46	0.895	Dimeric
8	Streptomyces griseus SgrAI	3mq6-1	24	0.905	Dimeric
92	B1 domain of streptococcal protein G	1q10-1	25	0.499	Dimeric
46	Sulfolobus islandicus rudivirus 1 ORF131	2x5h-1	23	0.615	Dimeric
103	Human ZIP kinase	2j90-1	15	0.804	Dimeric
97	Bacillus stearothermophilus sporulation response regulator Spo0A	1dz3-1	18	0.852	Dimeric
15	Focal adhesion targeting domain of chordate focal adhesion kinase	1k04-1	37	0.895	Dimeric
11	Human JARID1A C-terminal PHD finger	3gl6-1	15	0.503	Polymeric
21	Human death associated protein kinase 3	3bqr-1	18	0.793	Dimeric
49	Bacterial FtsZ	1w5f-1	119	0.780	Dimeric
86	Ligand-binding domain of Transcription Factor RXR?	1xiu-1	10	0.632	Dimeric
45	Peroxiredoxin 5	1oc3-1	11	0.649	Dimeric
22	Bacterial Phosphocarrier Protein HPr	3le5-1	15	0.741	Polymeric
13	Orotate phosphoribosyltransferase	3n2l-2	19	0.727	Dimeric
50	Variable fragment domain of mammalian antibody	1nqb-1	118	0.738	Oligomeric
64	Bacteriophage P1 Doc Toxin	3dd9-1	41	0.802	Dimeric
24	Human ribonuclease 1	1h8x-1	22	0.769	Dimeric
98	CAP-Gly domain of human dynactin-1	2hl3-1	12	0.905	Dimeric
32	Cell adhesion domain of mammalian CD2	1a64-1	43	0.920	Dimeric
33	Ribonuclease A, C-terminal Dimer	1f0v-2	12	0.913	Dimeric
70	Bacterial phosphocarrier protein C-terminus Swap	1y50-1	35	0.865	Dimeric
35	Ribonuclease A, C-terminal Trimer	1js0-2	14	0.546	Oligomeric
6	Entamoeba histolytica calcium-binding protein; EF-HAND	2nxq-2	28	0.496	Oligomeric
113	Human saposin C/D	2z9a-1	31	0.638	Dimeric
108	CARD domain of human Nod1	2nz7-1	11	0.615	Dimeric
41	Human Mst1/Mst2 kinase	2j7t-1	18	0.686	Dimeric
112	Yeast GCN4 leucine zipper	1u9h-1	7	0.022	Oligomeric
28	Bacterial cold-shock protein	2hax-1	29	0.901	Dimeric
114	Cathelin-like domain of sus scrofa protegrin	1lxe-1	35	0.947	Dimeric
95	SH2 domain of human nck1/2 adaptor protein	2ci8-1	43	0.897	Dimeric
26	Human anti-apoptotic protein Bcl-2	2p1l-1	23	0.811	Dimeric
109	Griffithsin	2nu5-1	17	0.690	Dimeric
81	Human Foxp1/2 Transcription Factor	2a07-1	33	0.774	Dimeric
85	Rabbit muscle aldolase	3lge-1	11	0.207	Oligomeric
4	Cyclophilin	2c3b-1	15	0.650	Dimeric
100	Prion protein	1i4m-1	35	0.767	Dimeric
39	HIV entry inhibitor Griffithsin	2gux-1	22	0.621	Dimeric
91	Mouse NF-?B RelB	1zk9-1	45	0.904	Dimeric
37	Human Cystatin C/D	1r4c-1	47	0.956	Dimeric
106	Motor domain of mammalian KIF2C	1v8k-1	18	0.324	Dimeric
34	Bovine seminal ribonuclease, N-terminal Dimer	1y92-1	16	0.781	Dimeric
25	Human adenosine kinase	2i6a-1	8	0.542	Dimeric
77	Yeast aminoacyl-tRNA synthetase complex	2hqt-1	13	0.695	Dimeric
52	Bacterioides thioredoxin	3hxs-1	20	0.904	Dimeric
61	Proteobacterial 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase	1vh8-7	22	0.492	Polymeric
60	Escherichia coli DraE/DaaE adhesins	2w5p-2	10	0.350	Oligomeric
111	Human CAP-Gly domain	2z0w-1	10	0.834	Dimeric
62	HIV-1 envelope protein gp41	1qr9-1	24	0.092	Oligomeric
2	NGF-binding domain of human nerve growth factor receptors	1wwa-1	15	0.866	Dimeric
65	SH3 domain	3fj5-1	28	0.780	Dimeric
31	Artifically-mutated finegoldia magna protein L	1jml-1	10	0.718	Dimeric
67	Staphylococcus aureus nuclease C-terminus Swap	1snd-1	23	0.657	Dimeric
3	SH2 domain of human Grb2	2aob-1	28	0.819	Dimeric
68	Staphylococcus aureus nuclease N-terminus Swap	3owf-1	15	0.850	Dimeric
104	C-terminal SH3 domain of human CrkL	2bzy-1	13	0.938	Dimeric
94	Anemone fluorescent protein asFP595	2a50-6	7	0.395	Dimeric
20	Cytochrome C Trimeric Swap	3nbt-1	23	0.650	Oligomeric
89	C-terminal domain of SARS-CoV main protease	3ebn-1	24	0.865	Dimeric
96	Bacterial Arsenate reductase azurin	3fsv-1	10	0.730	Dimeric
59	Artificially-mutated loop from human fibronectin type III domain	2rbl-1	28	0.786	Dimeric
105	G-protein signaling domain of mammalian RGS6/7/9	2es0-1	35	0.873	Dimeric
57	Angiosperm mannose-binding lectin	1msa-1	11	0.522	Dimeric
23	Mammalian Aurora A	3dj6-1	19	0.463	Dimeric
12	Acyl-CoA binding protein	3epy-1	39	0.837	Dimeric
53	HIV-1 capsid C-terminal domain	2ont-1	28	0.675	Dimeric
93	Barnase	1yvs-1	36	0.774	Oligomeric
36	SH2 domain of human Growth factor receptor-bound protein 2 (Grb2)	2h46-1	30	0.925	Dimeric
7	Nostoc ellipsosporum cyanovirin-N	1l5e-1	49	0.888	Dimeric
18	N-terminal domain of Saccharomyces cerevisiae t-SNARE protein tlg1	2c5j-1	23	0.844	Dimeric
9	Plantal dihydroflavanol 4-reductase	2rh8-1	13	0.222	Polymeric
75	ZNF UBP domain of human IsoT	2g45-1	23	0.861	Dimeric
48	Cap-binding domain of mammalian PARN	3ctr-1	49	0.436	Polymeric
30	Human stefin A/B	2oct-1	45	0.930	Dimeric
44	Human p22phox-p47phox complex	1ov3-1	49	0.856	Dimeric
82	Mammalian odorant binding protein	1hn2-1	34	0.671	Dimeric
55	Shewanella putrefaciens DUF442	3gxg-1	10	0.835	Dimeric
56	Type III secretory domain of yersinia YopH	1k46-1	26	0.836	Dimeric
10	Plantal calcium-binding pollen allergen	2opo-1	38	0.617	Dimeric
42	Diphtheria toxin	1sgk-1	156	0.839	Dimeric
40	Human Mst1/Mst2 kinase	2jfl-1	26	0.687	Dimeric
88	Human cd47 membrane protein	2vsc-1	14	0.862	Dimeric

3D Domain Swap Systems - ProSwap - Wodak Lab