2VHF: CYLD USP domain

Structure of the CYLD USP domain. Determined by X-ray diffraction at 2.8 Å resolution. Released 11 Mar 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 5,265
Mol. weight: 86.95 kDa
Ligands: ZN
Released: 11 Mar 2008

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

Secondary structure: helices and β-sheets

2VHF contains 47 α-helices and 49 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: 29 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	584-586	3
β-strand	589-590	2	1
β-strand	593-594	2	2
α-helix	595-596	2
α-helix	601-611	11
β-strand	614	1	3
α-helix	615-617	3
α-helix	618-622	5
α-helix	623-625	3
α-helix	633-637	5
α-helix	638-645	8
α-helix	646-650	5
β-strand	653-654	2	2
α-helix	656-669	14
α-helix	682-686	5
α-helix	687-694	8
α-helix	696-698	3
β-strand	700-704	5	4
α-helix	708-709	2
β-strand	710-712	3	4
β-strand	715-716	2	1
β-strand	729	1	5
α-helix	730-741	12
β-strand	743-745	3	4
β-strand	751-755	5	1
α-helix	756-757	2
β-strand	770	1	5
β-strand	774-775	2	1
α-helix	778-780	3
β-strand	781	1	4
α-helix	786	1
β-strand	787	1	6
α-helix	788	1
β-strand	794	1	6
β-strand	797-798	2	7
α-helix	800-802	3
β-strand	815-816	2	7
α-helix	818-824	7
α-helix	828-830	3
β-strand	836-837	2	7
α-helix	838-839	2
α-helix	858	1
β-strand	859-868	10	1
β-strand	871-877	7	1
β-strand	885-889	5	1
β-strand	905-908	4	1
α-helix	911-914	4
α-helix	920-925	6
α-helix	928-930	3
α-helix	935-940	6
β-strand	942	1	1
β-strand	944-948	5	1
α-helix	950-952	3
β-strand	953	1	3

Chain B: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	589-590	2	8
β-strand	593-594	2	9
α-helix	601-611	11
β-strand	614	1	10
α-helix	619-622	4
α-helix	633-642	10
α-helix	645-650	6
β-strand	653-654	2	9
α-helix	657-669	13
α-helix	682-689	8
β-strand	700-704	5	11
α-helix	708-709	2
β-strand	710-712	3	11
β-strand	715-716	2	8
β-strand	729	1	12
α-helix	730-740	11
β-strand	743-745	3	11
β-strand	751-755	5	8
α-helix	756-757	2
β-strand	770	1	12
β-strand	774-776	3	8
α-helix	778-780	3
β-strand	781	1	11
β-strand	787	1	13
β-strand	794	1	13
β-strand	797-798	2	14
α-helix	800-802	3
α-helix	813-814	2
β-strand	815-816	2	14
α-helix	818-824	7
α-helix	828-830	3
β-strand	836-837	2	14
α-helix	844-846	3
β-strand	858-868	11	8
β-strand	871-877	7	8
β-strand	885-889	5	8
β-strand	905-908	4	8
α-helix	912-915	4
α-helix	921-923	3
α-helix	936-940	5
β-strand	942-948	7	8
β-strand	953	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase cyld	A, B	protein	374	HOMO SAPIENS	Q9NQC7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2VHF_1 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD (chains A, B)
GLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSVLDTVLLRPKEKNDVEYYSETQELLRT
EIVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHHILRVEPLLKI
RSAGQKVQDCYFYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKD
FKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCNT
QVHLHPKRLNHKYNPVSLPKDLPDWDWRHGCIPCQNMELFAVLCIETSHYVAFVKYGKDD
SAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDLHSLDSRRIQGCARRLLCDA
YMCMYQSPTMSLYK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

The Structure of the Cyld Usp Domain Explains its Specificity for Lys63-Linked Polyubiquitin and Reveals a B-Box Module. Komander, D., Lord, C.J., Scheel, H. et al. Mol Cell Biol (2008) 29:451. DOI 10.1016/J.MOLCEL.2007.12.018 · PubMed

Other PDB entries of the same protein (UniProt Q9NQC7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OWD 1.71 Å, Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group
9TMK 1.8 Å, Structure of CYLD CAP-Gly2 bound to Listeria effector protein InlC
7OWC 1.85 Å, Structure of CYLD CAP-Gly3 (467-565) bound to Ub; orthorhobic space group
1IXD Solution structure of the CAP-GLY domain from human cylindromatosis tomour-suppressor CYLD
1WHL Solution structure of the 1st CAP-Gly domain in human cylindromatosis tumor suppressor…
1WHM Solution structure of the 2nd CAP-Gly domain in human cylindromatosis tumor suppressor…

Browse structure collections

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