2VFJ: A20 Ovarian Tumour (OTU) domain

Structure of the A20 Ovarian Tumour (OTU) domain. Determined by X-ray diffraction at 3.2 Å resolution. Released 4 Dec 2007.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 10,203
Mol. weight: 172.82 kDa
Ligands: MG
Released: 4 Dec 2007

Explore 2VFJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VFJ contains 71 α-helices and 88 β-strands across 4 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, 22 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	50	1	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	121-131	11
α-helix	136-148	13
α-helix	164-174	11
α-helix	179-180	2
α-helix	189-191	3
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
β-strand	279-280	2	9
β-strand	282	1	9
β-strand	285	1	8
β-strand	288	1	6
α-helix	295-297	3
α-helix	299-306	8
β-strand	309-316	8	7
β-strand	321-329	9	7
α-helix	330-332	3
α-helix	341-358	18

Chain B: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-28	14
β-strand	29-30	2	10
α-helix	36-38	3
β-strand	39-40	2	10
α-helix	43-45	3
β-strand	50	1	11
α-helix	58-68	11
β-strand	69	1	12
α-helix	71-79	9
β-strand	89	1	13
β-strand	92-94	3	14
β-strand	95	1	12
α-helix	103-113	11
α-helix	121-131	11
α-helix	136-148	13
α-helix	164-174	11
α-helix	189-191	3
α-helix	193-203	11
β-strand	207-210	4	15
β-strand	231-233	3	15
α-helix	240-242	3
β-strand	248-253	6	15
β-strand	256-259	4	15
β-strand	260-262	3	14
β-strand	263	1	11
β-strand	270	1	13
β-strand	272-274	3	16
β-strand	276	1	17
β-strand	279-280	2	18
β-strand	282	1	18
β-strand	285	1	17
β-strand	288	1	15
α-helix	295-297	3
α-helix	299-306	8
β-strand	309-313	5	16
β-strand	324-329	6	16
α-helix	330-333	4
α-helix	341-357	17

Chain C: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	19
α-helix	36-38	3
β-strand	39-40	2	19
α-helix	43-45	3
β-strand	50	1	20
α-helix	58-68	11
β-strand	69	1	21
α-helix	71-79	9
β-strand	89	1	22
β-strand	92-94	3	23
β-strand	95	1	21
α-helix	103-113	11
α-helix	121-131	11
α-helix	136-148	13
α-helix	164-174	11
α-helix	179-180	2
α-helix	189-191	3
α-helix	193-203	11
β-strand	207-210	4	24
β-strand	231-233	3	24
α-helix	240-242	3
β-strand	249-253	5	24
β-strand	256-259	4	24
β-strand	260-262	3	23
β-strand	263	1	20
β-strand	270	1	22
β-strand	272-274	3	25
β-strand	276	1	26
β-strand	279-280	2	27
β-strand	282	1	27
β-strand	285	1	26
β-strand	288	1	24
α-helix	295-297	3
α-helix	299-306	8
β-strand	309-313	5	25
β-strand	324-329	6	25
α-helix	330-332	3
α-helix	341-357	17

Chain D: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-27	13
β-strand	29-30	2	28
α-helix	36-38	3
β-strand	39-40	2	28
α-helix	43-45	3
β-strand	50	1	29
α-helix	58-68	11
β-strand	69	1	30
α-helix	71-79	9
β-strand	89	1	31
β-strand	92-94	3	32
β-strand	95	1	30
α-helix	103-113	11
α-helix	121-131	11
α-helix	136-148	13
α-helix	164-174	11
α-helix	179-180	2
α-helix	189-191	3
α-helix	193-203	11
β-strand	207-210	4	33
β-strand	231-233	3	33
α-helix	240-242	3
β-strand	248-253	6	33
β-strand	256-259	4	33
β-strand	260-262	3	32
β-strand	263	1	29
β-strand	270	1	31
β-strand	272-274	3	34
β-strand	276	1	35
β-strand	279	1	36
β-strand	282	1	36
β-strand	285	1	35
β-strand	288	1	33
α-helix	295-297	3
α-helix	299-306	8
β-strand	309-313	5	34
β-strand	324-329	6	34
α-helix	330-332	3
α-helix	341-358	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C, D	protein	366	HOMO SAPIENS	P21580 (AlphaFold model)

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

>2VFJ_1 TUMOR NECROSIS FACTOR (chains A, B, C, D)
MAEQVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQF
REIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDL
VLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTP
MARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPA
QECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKE
KLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQENS
EQGRRE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of the A20 Otu Domain and Mechanistic Insights Into Deubiquitination. Komander, D., Barford, D. Biochem J (2008) 409:77. DOI 10.1042/BJ20071399 · 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
5V3B 3.0 Å, Human A20 OTU domain (WT) with acetamidylated C103

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