4WLP: UCH37-NFRKB Inhibited Deubiquitylating Complex

Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 4 Mar 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,352
Mol. weight: 49.95 kDa
Released: 4 Mar 2015

Explore 4WLP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WLP contains 22 α-helices and 11 β-strands across 2 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: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	15-24	10
β-strand	28	1	1
β-strand	30-34	5	2
α-helix	40-44	5
α-helix	47	1
β-strand	49-56	8	2
β-strand	68	1	2
α-helix	72-75	4
α-helix	85-87	3
α-helix	88-97	10
β-strand	106	1	1
α-helix	109-117	9
α-helix	123-132	10
α-helix	134-147	14
α-helix	159-161	3
β-strand	164-171	8	2
β-strand	174-179	6	2
β-strand	186-190	5	2
β-strand	192	1	3
β-strand	195	1	3
α-helix	197-214	18
β-strand	219-225	7	2
α-helix	227-240	14
α-helix	256-288	33
α-helix	292-304	13
α-helix	308-320	13

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	42-44	3
α-helix	46-52	7
α-helix	55-60	6
α-helix	64-73	10
α-helix	81-94	14
α-helix	103-112	10
α-helix	118-151	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase isozyme L5	A	protein	317	Homo sapiens	Q9Y5K5 (AlphaFold model)
Nuclear factor related to kappa-B-binding protein	B	protein	114	Homo sapiens	Q6P4R8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4WLP_1 Ubiquitin carboxyl-terminal hydrolase isozyme L5 (chains A)
AGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEP
AGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAA
MKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREG
PIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAE
EPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAE
HQQLIPLVEKAKEKQNA

Sequence of entity 2 (B), FASTA

>4WLP_2 Nuclear factor related to kappa-B-binding protein (chains B)
EDLLEDPEIFFDVVSLSTWQEVLSDSQREHLQQFLPQFPEDSAEQQNELILALFSGENFR
FGNPLHIAQKLFRDGHFNPEVVKYRQLCFKSQYKRYLNSQQQYFHRLLKQILAS

Primary citation

Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase. VanderLinden, R.T., Hemmis, C.W., Schmitt, B. et al. Mol Cell (2015) 57:901-911. DOI 10.1016/j.molcel.2015.01.016 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5K5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RII 2.0 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
3A7S 2.2 Å, Catalytic domain of UCH37
3TB3 2.3 Å, Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted
4UEL 2.3 Å, UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
3RIS 2.4 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
9E7K 2.41 Å, Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in…
4UEM 2.82 Å, UCH-L5 in complex with the RPN13 DEUBAD domain
3IHR 2.95 Å, Crystal Structure of Uch37
4UF6 3.69 Å, UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G
4UF5 3.7 Å, Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G

Browse structure collections

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