5V3B: Tumor necrosis factor alpha-induced protein 3

Human A20 OTU domain (WT) with acetamidylated C103. Determined by X-ray diffraction at 3.0 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,207
Mol. weight: 258.96 kDa
Released: 21 Mar 2018

Explore 5V3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V3B contains 122 α-helices and 118 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: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-28	14
β-strand	29	1	1
α-helix	36-38	3
β-strand	40	1	1
α-helix	43-45	3
β-strand	50	1	2
α-helix	58-68	11
β-strand	69	1	3
α-helix	71-79	9
β-strand	89	1	4
α-helix	90-91	2
β-strand	92-94	3	5
β-strand	95	1	3
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	164-175	12
α-helix	193-203	11
β-strand	207-210	4	6
β-strand	231-233	3	6
α-helix	240-242	3
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	7
β-strand	276	1	8
α-helix	284	1
β-strand	285	1	8
α-helix	286-287	2
β-strand	288	1	6
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-314	6	7
β-strand	323-329	7	7
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-356	16

Chain B: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-28	14
β-strand	29-30	2	9
α-helix	36-38	3
β-strand	39-40	2	9
α-helix	43-45	3
α-helix	58-68	11
β-strand	69	1	10
α-helix	71-79	9
β-strand	89	1	11
α-helix	90-91	2
β-strand	92-94	3	12
β-strand	95	1	10
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	161-175	15
α-helix	193-203	11
β-strand	207-210	4	13
β-strand	231-233	3	13
α-helix	240-242	3
β-strand	248-253	6	13
β-strand	256-259	4	13
β-strand	260-262	3	12
β-strand	270	1	11
β-strand	272-274	3	14
β-strand	276-279	4	15
β-strand	282-285	4	15
α-helix	286-287	2
β-strand	288	1	13
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-314	6	14
β-strand	323-329	7	14
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-355	15

Chain C: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-28	14
β-strand	29	1	16
α-helix	36-38	3
β-strand	40	1	16
α-helix	43-45	3
β-strand	50	1	17
α-helix	58-68	11
β-strand	69	1	18
α-helix	71-79	9
β-strand	89	1	19
α-helix	90-91	2
β-strand	92-94	3	20
β-strand	95	1	18
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	164-175	12
α-helix	193-203	11
β-strand	207-211	5	21
β-strand	231-233	3	21
α-helix	240-242	3
β-strand	248-253	6	21
β-strand	256-259	4	21
β-strand	260-262	3	20
β-strand	263	1	17
β-strand	270	1	19
β-strand	272-274	3	22
β-strand	276-279	4	23
β-strand	282-285	4	23
α-helix	286-287	2
β-strand	288	1	21
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-313	5	22
β-strand	324-329	6	22
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-355	15

Chain D: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-28	14
β-strand	29	1	24
α-helix	36-38	3
β-strand	40	1	24
α-helix	43-45	3
β-strand	50	1	25
α-helix	58-68	11
β-strand	69	1	26
α-helix	71-79	9
β-strand	89	1	27
α-helix	90-91	2
β-strand	92-94	3	28
β-strand	95	1	26
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	164-175	12
α-helix	193-203	11
β-strand	207-210	4	29
β-strand	231-233	3	29
α-helix	240-242	3
β-strand	248-253	6	29
β-strand	256-259	4	29
β-strand	260-262	3	28
β-strand	263	1	25
β-strand	270	1	27
β-strand	272-274	3	30
β-strand	276-278	3	31
β-strand	283-285	3	31
α-helix	286-287	2
β-strand	288	1	29
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-315	7	30
β-strand	322-329	8	30
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-357	17

Chain E: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-28	14
β-strand	29	1	32
α-helix	36-38	3
β-strand	40	1	32
α-helix	43-45	3
β-strand	50	1	33
α-helix	58-68	11
β-strand	69	1	34
α-helix	71-79	9
β-strand	89	1	35
α-helix	90-91	2
β-strand	92-94	3	36
β-strand	95	1	34
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-149	14
α-helix	163-175	13
α-helix	193-203	11
β-strand	207-210	4	37
β-strand	231-233	3	37
α-helix	240-242	3
β-strand	248-253	6	37
β-strand	256-259	4	37
β-strand	260-262	3	36
β-strand	263	1	33
β-strand	270	1	35
β-strand	272-274	3	38
β-strand	276-277	2	39
β-strand	284-285	2	39
α-helix	286-287	2
β-strand	288	1	37
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-314	6	38
β-strand	323-329	7	38
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-355	15

Chain F: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-28	14
β-strand	29	1	40
α-helix	36-38	3
β-strand	40	1	40
α-helix	43-45	3
β-strand	50	1	41
α-helix	58-68	11
β-strand	69	1	42
α-helix	71-79	9
β-strand	89	1	43
α-helix	90-91	2
β-strand	92-94	3	44
β-strand	95	1	42
α-helix	96	1
α-helix	103-113	11
α-helix	121-131	11
α-helix	136-148	13
α-helix	164-175	12
α-helix	179-180	2
α-helix	193-203	11
β-strand	207-209	3	45
β-strand	231-233	3	45
α-helix	240-242	3
β-strand	248-253	6	45
β-strand	256-259	4	45
β-strand	260-262	3	44
β-strand	263	1	41
β-strand	270	1	43
β-strand	272-274	3	46
β-strand	276-277	2	47
β-strand	284-285	2	47
α-helix	286-287	2
β-strand	288	1	45
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-314	6	46
β-strand	323-329	7	46
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-357	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor alpha-induced protein 3	A, B, C, D, E, F	protein	366	Homo sapiens	P21580 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5V3B_1 Tumor necrosis factor alpha-induced protein 3 (chains A, B, C, D, E, F)
MAEQVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQF
REIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDL
VLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTP
MARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPA
QECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKE
KLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQENS
EQGRRE

Primary citation

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity. Zammit, N.W., Siggs, O.M., Gray, P.E. et al. Nat Immunol (2019) 20:1299-1310. DOI 10.1038/s41590-019-0492-0 · 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
5LRX 2.85 Å, Structure of A20 OTU domain bound to ubiquitin
2VFJ 3.2 Å, Structure of the A20 Ovarian Tumour (OTU) domain

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