6A73: Complex structure of CSN2 with IP6

Complex structure of CSN2 with IP6. Determined by X-ray diffraction at 2.45 Å resolution. Released 3 Jul 2019.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, Enterobacteria phage RB59
Chains: 2
Atoms: 4,973
Mol. weight: 72.14 kDa
Ligands: IHP
Released: 3 Jul 2019

Explore 6A73 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6A73 contains 34 α-helices and 12 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: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	34-42	9
α-helix	47-60	14
α-helix	65-82	18
α-helix	85-101	17
α-helix	105-119	15
α-helix	125-139	15
α-helix	147-172	26
β-strand	175-176	2	1
β-strand	177	1	2
β-strand	178-180	3	1
β-strand	186-189	4	1
β-strand	192-195	4	1
α-helix	200-211	12
β-strand	218	1	2
α-helix	221-241	21
α-helix	245-251	7
α-helix	254-267	14
α-helix	269-273	5
α-helix	276-283	8
α-helix	287-295	9
α-helix	298-302	5
α-helix	304-316	13

Chain B: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	34-42	9
α-helix	47-53	7
α-helix	54-59	6
α-helix	60-61	2
α-helix	66-82	17
α-helix	85-99	15
α-helix	105-119	15
α-helix	125-139	15
α-helix	147-172	26
β-strand	175-176	2	3
β-strand	177	1	4
β-strand	178-180	3	3
β-strand	186-189	4	3
β-strand	192-195	4	3
α-helix	200-211	12
β-strand	218	1	4
α-helix	221-241	21
α-helix	245-251	7
α-helix	254-267	14
α-helix	269-273	5
α-helix	276-283	8
α-helix	287-295	9
α-helix	298-302	5
α-helix	304-316	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
COP9 signalosome complex subunit 2,Endolysin	A, B	protein	304	Homo sapiens, Enterobacteria phage RB59	P00720, P61201 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6A73_1 COP9 signalosome complex subunit 2,Endolysin (chains A, B)
MNVDLENQYYNSKALKEDDPKAALSSFQKVLELEGEKGEWGFKALKQMIKINFKLTNFPE
MMNRYKQLLTYIRSAVTRNYSEKSINSILDYISTSKQMDLLQEFYETTLEALKDAKNDRL
WFKTNTKLGKLYLERNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL
DKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQM
GETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLHH
HHHH

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	2

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

Primary citation

Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome. Lin, H., Zhang, X., Liu, L. et al. Proc Natl Acad Sci U S A (2020) 117:4117-4124. DOI 10.1073/pnas.1911998117 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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