5LRX: A20 OTU domain

Structure of A20 OTU domain bound to ubiquitin. Determined by X-ray diffraction at 2.85 Å resolution. Released 19 Oct 2016.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,566
Mol. weight: 191.24 kDa
Released: 19 Oct 2016

Explore 5LRX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LRX contains 95 α-helices and 100 β-strands across 6 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: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-22	8
α-helix	25-28	4
β-strand	29-30	2	1
α-helix	36-38	3
β-strand	39-40	2	1
α-helix	43-45	3
α-helix	48-49	2
β-strand	50	1	2
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	3
α-helix	71-79	9
β-strand	89	1	4
β-strand	92-94	3	5
β-strand	95	1	3
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-149	14
α-helix	152-155	4
α-helix	161-175	15
α-helix	193-203	11
β-strand	207-211	5	6
β-strand	214-216	3	7
α-helix	217	1
β-strand	223-226	4	7
β-strand	231-233	3	6
α-helix	240-242	3
α-helix	247	1
β-strand	248-253	6	6
β-strand	256-259	4	6
β-strand	260-262	3	5
β-strand	263	1	2
β-strand	270	1	4
β-strand	272-274	3	8
β-strand	276-278	3	9
β-strand	283-285	3	9
α-helix	286-287	2
β-strand	288	1	6
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-316	8	8
β-strand	321-329	9	8
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-356	16

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-16	5	10
β-strand	22	1	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	55	1	11
α-helix	57-59	3
β-strand	66-71	6	10

Chain C: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	12
α-helix	36-38	3
β-strand	39-40	2	12
α-helix	43-45	3
β-strand	50	1	13
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	14
α-helix	71-79	9
β-strand	89	1	15
α-helix	90-91	2
β-strand	92-94	3	16
β-strand	95	1	14
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-147	12
α-helix	151-154	4
α-helix	161-174	14
α-helix	193-202	10
β-strand	207-211	5	17
β-strand	214-215	2	18
α-helix	216-217	2
β-strand	225-226	2	18
β-strand	231-233	3	17
α-helix	240-242	3
β-strand	248-253	6	17
β-strand	256-259	4	17
β-strand	260-262	3	16
β-strand	263	1	13
α-helix	264	1
β-strand	270	1	15
β-strand	272-274	3	19
β-strand	276-279	4	20
β-strand	282-285	4	20
α-helix	286-287	2
β-strand	288	1	17
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-314	6	19
β-strand	323-329	7	19
α-helix	330-333	4
α-helix	337-339	3
α-helix	341-358	18

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	21
β-strand	12-16	5	21
β-strand	22	1	22
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	21
β-strand	48-49	2	21
β-strand	55	1	22
α-helix	57-59	3
β-strand	66-71	6	21

Chain E: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-22	8
α-helix	26-28	3
β-strand	29-30	2	23
α-helix	36-38	3
β-strand	39-40	2	23
α-helix	43-45	3
β-strand	49-50	2	24
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	25
α-helix	71-79	9
β-strand	89	1	26
β-strand	92-94	3	24
β-strand	95	1	25
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-147	12
α-helix	164-174	11
α-helix	193-203	11
β-strand	207-210	4	27
β-strand	214-216	3	28
β-strand	224-226	3	28
β-strand	231-233	3	27
α-helix	240-242	3
α-helix	247	1
β-strand	248-253	6	27
β-strand	256-259	4	27
β-strand	260-263	4	24
β-strand	270	1	26
β-strand	272-274	3	29
β-strand	276-279	4	30
β-strand	282-285	4	30
α-helix	286-287	2
β-strand	288	1	27
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-315	7	29
α-helix	317-319	3
β-strand	322-329	8	29
α-helix	330-333	4
α-helix	337-339	3
α-helix	341-357	17

Chain F: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	31
β-strand	39-40	2	31
α-helix	43-45	3
β-strand	49-50	2	32
α-helix	58-68	11
β-strand	69	1	33
α-helix	71-79	9
β-strand	89	1	34
β-strand	92-94	3	32
β-strand	95	1	33
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	168-174	7
α-helix	193-203	11
β-strand	207-210	4	35
β-strand	214-216	3	36
β-strand	224-226	3	36
β-strand	231-233	3	35
α-helix	240-242	3
β-strand	248-252	5	35
β-strand	257-259	3	35
β-strand	260-263	4	32
β-strand	270	1	34
β-strand	272-274	3	37
β-strand	276-279	4	38
β-strand	282-285	4	38
α-helix	286-287	2
β-strand	288	1	35
α-helix	293-296	4
α-helix	299-306	8
β-strand	309-315	7	37
α-helix	317-319	3
β-strand	322-329	8	37
α-helix	330-333	4
α-helix	337-339	3
α-helix	341-355	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor alpha-induced protein 3	A, C	protein	371	Homo sapiens	P21580 (AlphaFold model)
Polyubiquitin-B	B, D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Tumor necrosis factor alpha-induced protein 3	E, F	protein	371	Homo sapiens	P21580 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5LRX_1 Tumor necrosis factor alpha-induced protein 3 (chains A, C)
GPLGSMAEQVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQ
FCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGV
QDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMA
STDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLP
LHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPE
NEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKK
WQENSEQGRRE

Sequence of entity 2 (B, D), FASTA

>5LRX_2 Polyubiquitin-B (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Sequence of entity 3 (E, F), FASTA

>5LRX_3 Tumor necrosis factor alpha-induced protein 3 (chains E, F)
GPLGSMAEQVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQ
FCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGV
QDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMA
STDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLP
LHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPE
NEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKK
WQENSEQGRRE

Primary citation

Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Mevissen, T.E., Kulathu, Y., Mulder, M.P. et al. Nature (2016) 538:402-405. DOI 10.1038/nature19836 · PubMed

Other PDB entries of the same protein (UniProt P21580 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VUX 1.7 Å, Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II
3ZJE 1.84 Å, A20 OTU domain in reversibly oxidised (SOH) state
3ZJD 1.87 Å, A20 OTU domain in reduced, active state at 1.87 A resolution
3ZJG 1.92 Å, A20 OTU domain with irreversibly oxidised Cys103 from 60 min H2O2 soak.
3VUW 1.95 Å, Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I
3VUY 1.98 Å, Crystal structure of A20 ZF7 in complex with linear tetraubiquitin
3ZJF 2.2 Å, A20 OTU domain with irreversibly oxidised Cys103 from 270 min H2O2 soak.
3DKB 2.5 Å, Crystal Structure of A20, 2.5 angstrom
3OJ3 2.5 Å, Crystal structure of the A20 ZnF4 and ubiquitin complex
5V3P 2.5 Å, Human A20 OTU domain (I325N) with acetamidylated C103
5V3B 3.0 Å, Human A20 OTU domain (WT) with acetamidylated C103
2VFJ 3.2 Å, Structure of the A20 Ovarian Tumour (OTU) domain

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