2GWF: USP8-NRDP1 complex

Structure of a USP8-NRDP1 complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 6 Jun 2006.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,388
Mol. weight: 98.29 kDa
Released: 6 Jun 2006

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

Secondary structure: helices and β-sheets

2GWF contains 57 α-helices and 43 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	182-183	2	1
α-helix	185-193	9
β-strand	199-203	5	1
α-helix	207-212	6
β-strand	215	1	2
β-strand	219-220	2	1
α-helix	223-225	3
α-helix	232-237	6
α-helix	241-248	8
β-strand	255-259	5	1
α-helix	265-267	3
α-helix	273-282	10
β-strand	295-297	3	1
α-helix	300-307	8
α-helix	309-311	3
β-strand	312	1	2

Chain B: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	198-205	8
α-helix	207	1
β-strand	208	1	3
β-strand	209-211	3	4
α-helix	214-216	3
β-strand	217-218	2	3
α-helix	223-235	13
α-helix	240-248	9
α-helix	252-254	3
α-helix	257-259	3
α-helix	262-272	11
β-strand	278-279	2	3
α-helix	280	1
β-strand	285-289	5	3
α-helix	290-292	3
β-strand	305-310	6	3
β-strand	314-316	3	4

Chain C: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	182-183	2	5
α-helix	185-193	9
β-strand	199-203	5	5
α-helix	207-212	6
β-strand	215	1	6
α-helix	218	1
β-strand	219-220	2	5
α-helix	223-225	3
α-helix	232-237	6
α-helix	241-247	7
β-strand	255-259	5	5
α-helix	265-267	3
α-helix	273-282	10
β-strand	295-297	3	5
α-helix	300-307	8
α-helix	309-311	3
β-strand	312	1	6

Chain D: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	193-205	13
α-helix	207	1
β-strand	208	1	7
β-strand	209-211	3	8
α-helix	214-216	3
β-strand	217-218	2	7
α-helix	223-235	13
α-helix	243-248	6
α-helix	252-254	3
α-helix	262-268	7
α-helix	269-274	6
β-strand	278-279	2	7
β-strand	285-289	5	7
α-helix	290-292	3
β-strand	305-310	6	7
β-strand	314-316	3	8

Chain E: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	182-183	2	9
α-helix	185-193	9
β-strand	199-203	5	9
α-helix	207-212	6
β-strand	215	1	10
α-helix	218	1
β-strand	219-220	2	9
α-helix	223-225	3
α-helix	232-237	6
α-helix	241-248	8
β-strand	255-259	5	9
α-helix	265-267	3
α-helix	273-282	10
β-strand	295-297	3	9
α-helix	300-307	8
α-helix	309-311	3
β-strand	312	1	10
β-strand	314	1	10

Chain F: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	197-205	9
α-helix	207	1
β-strand	208	1	11
β-strand	209-211	3	12
α-helix	214-216	3
β-strand	217-218	2	11
α-helix	223-235	13
α-helix	240-248	9
α-helix	252-254	3
α-helix	262-268	7
α-helix	269-274	6
β-strand	277-279	3	11
β-strand	285-289	5	11
α-helix	290-292	3
β-strand	305-310	6	11
β-strand	314-316	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 8	A, C, E	protein	157	Homo sapiens	P40818 (AlphaFold model)
RING finger protein 41	B, D, F	protein	134	Homo sapiens	Q9H4P4 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>2GWF_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A, C, E)
MGSSHHHHHHSSGLVPRGSGAITAKELYTMMTDKNISLIIMDARRMQDYQDSCILHSLSV
PEEAISPGVTASWIEAHLPDDSKDTWKKRGNVEYVVLLDWFSSAKDLQIGTTLRSLKDAL
FKWESKTVLRNEPLVLEGGYENWLLCYPQYTTNAKVT

Sequence of entity 2 (B, D, F), FASTA

>2GWF_2 RING finger protein 41 (chains B, D, F)
SSGLVPRGSTIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIV
NELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQE
PGLVMIFAHGVEEI

Primary citation

Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8). Avvakumov, G.V., Walker, J.R., Xue, S. et al. J Biol Chem (2006) 281:38061-38070. DOI 10.1074/jbc.M606704200 · PubMed

Other PDB entries of the same protein (UniProt P40818 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6F09 1.59 Å, Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide
8ADM 1.7 Å, Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer
2GFO 2.0 Å, Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8
2A9U 2.1 Å, Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)
8XPN 2.1 Å, The Crystal Structure of USP8 from Biortus.
3N3K 2.6 Å, The catalytic domain of USP8 in complex with a USP8 specific inhibitor
8Y9A 3.1 Å, The Crystal Structure of USP8 from Biortus.
1WHB Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8…

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