4KSL: Gumby/Fam105B

Gumby/Fam105B in complex with linear di-ubiquitin. Determined by X-ray diffraction at 2.83 Å resolution. Released 5 Jun 2013.

Method: X-ray diffraction
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 24
Atoms: 40,089
Mol. weight: 593.93 kDa
Released: 5 Jun 2013

Explore 4KSL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KSL contains 286 α-helices and 312 β-strands across 24 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	1
α-helix	83-85	3
β-strand	86-87	2	2
α-helix	88-95	8
α-helix	101-116	16
β-strand	119-121	3	2
α-helix	122	1
β-strand	123	1	1
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-156	5
α-helix	157-164	8
α-helix	166-169	4
α-helix	184-203	20
α-helix	208-218	11
α-helix	222-248	27
α-helix	255-260	6
α-helix	269-275	7
α-helix	277-279	3
β-strand	280	1	3
β-strand	284	1	3
α-helix	288-298	11
β-strand	301-306	6	4
α-helix	307-309	3
β-strand	316-319	4	4
β-strand	329-334	6	4
β-strand	341	1	4
β-strand	342-344	3	2

Chain B: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	9
α-helix	83-85	3
β-strand	86-87	2	10
α-helix	88-95	8
α-helix	101-116	16
β-strand	119-121	3	10
α-helix	122	1
β-strand	123	1	9
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-156	5
α-helix	157-164	8
α-helix	166-170	5
α-helix	184-203	20
α-helix	208-218	11
α-helix	222-248	27
α-helix	255-261	7
α-helix	269-275	7
α-helix	277-279	3
α-helix	288-298	11
β-strand	301-306	6	11
α-helix	307-309	3
β-strand	316-319	4	11
β-strand	329-334	6	11
β-strand	341	1	11
β-strand	342-344	3	10

Chain C: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	12
β-strand	12-17	6	12
β-strand	22	1	13
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	12
β-strand	48-49	2	12
β-strand	55	1	13
α-helix	57-59	3
β-strand	66-69	4	12
β-strand	1001-1007	7	14
β-strand	1012-1017	6	14
β-strand	1022	1	15
α-helix	1023-1034	12
α-helix	1038-1040	3
β-strand	1041-1045	5	14
β-strand	1048-1049	2	14
α-helix	1050	1
β-strand	1052	1	16
β-strand	1054	1	16
β-strand	1055	1	15
β-strand	1066-1071	6	14

Chain D: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	5
β-strand	48-49	2	5
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-69	4	5
β-strand	1001-1007	7	7
β-strand	1012-1017	6	7
β-strand	1022	1	8
α-helix	1023-1034	12
α-helix	1038-1040	3
β-strand	1041-1045	5	7
β-strand	1048-1049	2	7
α-helix	1050	1
β-strand	1055	1	8
β-strand	1066-1071	6	7

Chain E: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	17
α-helix	83-85	3
β-strand	86-87	2	18
α-helix	88-95	8
α-helix	101-116	16
β-strand	119-121	3	18
α-helix	122	1
β-strand	123	1	17
α-helix	124	1
β-strand	126	1	19
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-156	5
α-helix	157-164	8
α-helix	166-170	5
α-helix	184-203	20
α-helix	208-218	11
α-helix	223-248	26
α-helix	255-261	7
α-helix	269-275	7
α-helix	277-279	3
β-strand	280	1	20
β-strand	284	1	20
α-helix	288-298	11
β-strand	301-306	6	21
α-helix	307-309	3
β-strand	316-319	4	21
β-strand	329-334	6	21
β-strand	341	1	21
β-strand	342-344	3	18

Chains F, J and L: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	22
β-strand	12-17	6	22
β-strand	22	1	23
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	22
β-strand	48-49	2	22
β-strand	55	1	23
α-helix	57-59	3
β-strand	66-69	4	22
β-strand	1001-1007	7	19
β-strand	1012-1017	6	19
β-strand	1022	1	24
α-helix	1023-1034	12
α-helix	1038-1040	3
β-strand	1041-1045	5	19
β-strand	1048-1049	2	19
α-helix	1050	1
β-strand	1055	1	24
β-strand	1066-1071	6	19

Chain G: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	25
α-helix	83-85	3
β-strand	86-87	2	26
α-helix	88-95	8
α-helix	101-116	16
β-strand	119-121	3	26
α-helix	122	1
β-strand	123	1	25
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-156	5
α-helix	157-164	8
α-helix	166-170	5
α-helix	184-203	20
α-helix	208-218	11
α-helix	223-248	26
α-helix	255-260	6
α-helix	269-275	7
α-helix	277-279	3
β-strand	280	1	27
β-strand	284	1	27
α-helix	288-298	11
β-strand	301-306	6	28
α-helix	307-309	3
β-strand	316-319	4	28
β-strand	329-334	6	28
β-strand	341	1	28
β-strand	342-344	3	26

Chain H: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	29
β-strand	12-16	5	29
β-strand	22	1	30
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	29
β-strand	48-49	2	29
β-strand	55	1	30
β-strand	66-69	4	29
β-strand	1001-1007	7	31
β-strand	1012-1017	6	31
β-strand	1022	1	32
α-helix	1023-1034	12
α-helix	1038-1040	3
β-strand	1041-1045	5	31
β-strand	1048-1049	2	31
α-helix	1050	1
β-strand	1055	1	32
β-strand	1066-1071	6	31

14 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein FAM105B	A, B, E, G, I, K, M, O, Q, S, U, W	protein	276	Homo sapiens	Q96BN8 (AlphaFold model)
Polyubiquitin-C	C, D, F, H, J, L, N, P, R, T, V, X	protein	156	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B, E, G, I, K, M, O, Q, S, U, W), FASTA

>4KSL_1 Protein FAM105B (chains A, B, E, G, I, K, M, O, Q, S, U, W)
GSRLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYAALRATLF
QAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLGLKFDGKNEDLVDKIKESLTLLR
KKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFF
SVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFI
TVYPTDPPKDWPVVTLIAEDDRHYNIPVRVCEETSL

Sequence of entity 2 (C, D, F, H, J, L, N, P, R, T, V, X), FASTA

>4KSL_2 Polyubiquitin-C (chains C, D, F, H, J, L, N, P, R, T, V, X)
GAMGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Primary citation

The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis. Rivkin, E., Almeida, S.M., Ceccarelli, D.F. et al. Nature (2013) 498:318-324. DOI 10.1038/nature12296 · PubMed

Other PDB entries of the same protein (UniProt Q96BN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZNV 1.3 Å, Crystal structure of the OTU domain of OTULIN at 1.3 Angstroms.
3ZNX 1.35 Å, Crystal structure of the OTU domain of OTULIN D336A mutant
4KSJ 1.6 Å, Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom
6I9C 1.77 Å, Structure of the OTU domain of OTULIN G281R mutant
3ZNZ 1.9 Å, Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin
6SAK 2.0 Å, Structure of the OTULINcat C129A - SNX27 PDZ domain complex.
9LZX 2.0 Å, Crystal structure of the OTU domain of OTULIN in complex with 11B6
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
4KSK 2.4 Å, Gumby/Fam105B in complex with ubiquitin
4P0B 2.7 Å, Crystal structure of HOIP PUB domain in complex with OTULIN PIM
5OE7 2.95 Å, Structure of OTULIN bound to the Met1-linked diubiquitin activity probe

Browse structure collections

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