5V3P: Tumor necrosis factor alpha-induced protein 3

Human A20 OTU domain (I325N) with acetamidylated C103. Determined by X-ray diffraction at 2.5 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,786
Mol. weight: 258.97 kDa
Released: 21 Mar 2018

Explore 5V3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V3P contains 118 α-helices and 106 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, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	1
α-helix	36-38	3
β-strand	39-40	2	1
α-helix	43-45	3
β-strand	49-50	2	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	2
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	164-174	11
α-helix	193-203	11
β-strand	207-210	4	5
β-strand	231-233	3	5
α-helix	240-242	3
β-strand	248-253	6	5
β-strand	256-259	4	5
β-strand	260-263	4	2
β-strand	270	1	4
β-strand	272-274	3	6
β-strand	276-277	2	7
β-strand	284-285	2	7
α-helix	286-287	2
β-strand	288	1	5
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-312	4	6
α-helix	313-314	2
β-strand	325-329	5	6
α-helix	330-333	4
α-helix	337-339	3
α-helix	341-356	16

Chain B: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	8
α-helix	36-38	3
β-strand	39-40	2	8
α-helix	43-45	3
β-strand	49-50	2	9
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	10
α-helix	71-79	9
β-strand	89	1	11
β-strand	92-94	3	9
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	164-174	11
α-helix	193-203	11
β-strand	207-210	4	12
β-strand	231-233	3	12
α-helix	240-242	3
β-strand	248-253	6	12
β-strand	256-259	4	12
β-strand	260-263	4	9
β-strand	270	1	11
β-strand	272-274	3	13
β-strand	276	1	14
β-strand	285	1	14
α-helix	286-287	2
β-strand	288	1	12
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-310	2	13
β-strand	327-329	3	13
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-357	17

Chain C: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	15
α-helix	36-38	3
β-strand	39-40	2	15
α-helix	43-45	3
β-strand	49-50	2	16
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	17
α-helix	71-79	9
β-strand	89	1	18
β-strand	92-94	3	16
β-strand	95	1	17
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	164-174	11
α-helix	193-203	11
β-strand	207-210	4	19
β-strand	231-233	3	19
α-helix	240-242	3
β-strand	248-253	6	19
β-strand	256-259	4	19
β-strand	260-263	4	16
β-strand	270	1	18
β-strand	272-274	3	20
β-strand	276	1	21
β-strand	285	1	21
α-helix	286-287	2
β-strand	288	1	19
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-311	3	20
β-strand	326-329	4	20
α-helix	330-333	4
α-helix	337-339	3
α-helix	341-357	17

Chain D: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	22
α-helix	36-38	3
β-strand	39-40	2	22
α-helix	43-45	3
β-strand	49-50	2	23
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	24
α-helix	71-79	9
β-strand	89	1	25
β-strand	92-94	3	23
β-strand	95	1	24
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-148	13
α-helix	164-174	11
α-helix	193-203	11
β-strand	207-211	5	26
β-strand	231-233	3	26
α-helix	240-242	3
β-strand	248-253	6	26
β-strand	256-259	4	26
β-strand	260-263	4	23
β-strand	270	1	25
β-strand	272-274	3	27
α-helix	285-287	3
β-strand	288	1	26
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-311	3	27
β-strand	326-329	4	27
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-356	16

Chain E: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	28
β-strand	39-40	2	28
α-helix	43-45	3
α-helix	50-52	3
α-helix	58-68	11
β-strand	69	1	29
α-helix	71-79	9
β-strand	89	1	30
β-strand	93-94	2	31
β-strand	95	1	29
α-helix	96	1
α-helix	103-113	11
α-helix	121-132	12
α-helix	136-145	10
α-helix	164-174	11
α-helix	193-203	11
β-strand	207-210	4	32
β-strand	231-233	3	32
α-helix	240-242	3
β-strand	248-253	6	32
β-strand	256-259	4	32
β-strand	260-261	2	31
β-strand	270	1	30
β-strand	272-274	3	33
α-helix	285-287	3
β-strand	288	1	32
α-helix	293-297	5
α-helix	299-306	8
β-strand	309-310	2	33
β-strand	327-329	3	33
α-helix	331-333	3
α-helix	337-339	3
α-helix	341-357	17

Chain F: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	34
α-helix	36-38	3
β-strand	39-40	2	34
α-helix	43-45	3
β-strand	50	1	35
α-helix	51-52	2
α-helix	58-68	11
β-strand	69	1	36
α-helix	71-79	9
β-strand	92-94	3	37
β-strand	95	1	36
α-helix	96	1
α-helix	103-113	11
α-helix	121-129	9
α-helix	138-141	4
α-helix	193-203	11
β-strand	207-209	3	38
β-strand	231-233	3	38
α-helix	240-242	3
β-strand	248-253	6	38
β-strand	256-259	4	38
β-strand	260-262	3	37
β-strand	263	1	35
β-strand	273-274	2	39
β-strand	288	1	38
α-helix	293-297	5
α-helix	299-306	8
β-strand	309	1	39
β-strand	327-328	2	39
α-helix	329-333	5
α-helix	337-339	3
α-helix	341-352	12

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

>5V3P_1 Tumor necrosis factor alpha-induced protein 3 (chains A, B, C, D, E, F)
MAEQVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQF
REIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDL
VLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTP
MARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPA
QECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKE
KLLKEYLMVIEIPVQGWDHGTTHLNNAAKLDEANLPKEINLVDDYFELVQHEYKKWQENS
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
5LRX 2.85 Å, Structure of A20 OTU domain bound to ubiquitin
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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