4I6J: A ubiquitin ligase-substrate complex

A ubiquitin ligase-substrate complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 13 Mar 2013.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 8,435
Mol. weight: 129.29 kDa
Released: 13 Mar 2013

Explore 4I6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4I6J contains 56 α-helices and 28 β-strands across 3 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: 31 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
α-helix	37-43	7
β-strand	49-55	7	1
α-helix	67-85	19
β-strand	91-95	5	1
α-helix	102-109	8
β-strand	113-117	5	1
α-helix	122-136	15
β-strand	141-145	5	1
α-helix	153-159	7
α-helix	168-177	10
α-helix	179-189	11
α-helix	191-194	4
α-helix	202-207	6
α-helix	232-242	11
α-helix	245-248	4
α-helix	260-262	3
α-helix	270-275	6
α-helix	280-295	16
α-helix	302-305	4
α-helix	306-318	13
α-helix	338	1
β-strand	339	1	2
α-helix	340	1
α-helix	342-349	8
α-helix	356-368	13
α-helix	373-381	9
α-helix	382-386	5
β-strand	390	1	2
α-helix	392-402	11
α-helix	408-418	11
α-helix	435-440	6
α-helix	447-450	4
α-helix	452-454	3
α-helix	459-462	4
α-helix	465-467	3
α-helix	470-475	6
β-strand	480	1	3
β-strand	484	1	3
α-helix	491-510	20

Chain B: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	42-48	7
α-helix	53-59	7
α-helix	64-70	7
α-helix	73-76	4
β-strand	78-83	6	4
β-strand	89	1	2
α-helix	93-95	3
α-helix	96-106	11
β-strand	112-117	6	4
α-helix	121-131	11
β-strand	141-146	6	4
α-helix	151-154	4
α-helix	157-170	14
β-strand	176-178	3	4
α-helix	186-196	11
β-strand	202-204	3	4
α-helix	213-222	10
β-strand	228-232	5	4
α-helix	233-235	3
α-helix	238-245	8
β-strand	254-260	7	4
α-helix	274-283	10
β-strand	288-294	7	4
β-strand	312-315	4	4
α-helix	321-328	8
β-strand	336-339	4	4
α-helix	348-357	10
β-strand	363-366	4	4
β-strand	371-372	2	5
α-helix	373-382	10
α-helix	384-386	3
β-strand	389-392	4	4
β-strand	393	1	6
α-helix	394-396	3
β-strand	397-398	2	5
α-helix	405-416	12
β-strand	423	1	6

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	7
β-strand	15-16	2	7
α-helix	55-60	6
α-helix	97-109	13
α-helix	115-127	13
α-helix	132-137	6
α-helix	148-158	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cryptochrome-2	A	protein	544	Mus musculus	Q9R194 (AlphaFold model)
F-box/LRR-repeat protein 3	B	protein	428	Homo sapiens	Q9UKT7 (AlphaFold model)
S-phase kinase-associated protein 1	C	protein	163	Homo sapiens	P63208 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4I6J_1 Cryptochrome-2 (chains A)
MAAAAVVAATVPAQSMGADGASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFA
ASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDS
EPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMEL
PKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLD
KHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTP
PLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDA
IMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSC
SAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCII
GVDYPRPIVNHAETSRLNIERMKQIYQQLSRYRGLCLLASVPSCVEDLSHPVAEPGSSQA
GSIS

Sequence of entity 2 (B), FASTA

>4I6J_2 F-box/LRR-repeat protein 3 (chains B)
MKRGGRDSDRNSSEEGTAEKSKKLRTTNEHSQTCDWGNLLQDIILQVFKYLPLLDRAHAS
QVCRNWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSS
KESAEAACDILSQLVNCSLKTLGLISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKID
DTPVDDPSLKVLVANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDEL
LLALSSEKHVRLEHLRIDVVSENPGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEF
DPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPRLVELVVCANGLRPLDEELIRIAERCKN
LSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLIPDQKYSLEQIHWEVSKHLGRVW
FPDMMPTW

Sequence of entity 3 (C), FASTA

>4I6J_3 S-phase kinase-associated protein 1 (chains C)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Primary citation

SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket. Xing, W., Busino, L., Hinds, T.R. et al. Nature (2013) 496:64-68. DOI 10.1038/nature11964 · PubMed

Other PDB entries of the same protein (UniProt Q9R194 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7V8Y 1.9 Å, Crystal structure of mouse CRY2 in complex with SHP1703 compound
4MLP 1.94 Å, Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase
7V8Z 1.95 Å, Crystal structure of mouse CRY2 in complex with SHP656 compound
4I6G 2.2 Å, a vertebrate cryptochrome with FAD
6KX8 2.25 Å, Crystal structure of mouse Cryptochrome 2 in complex with TH301 compound
7EJ9 2.6 Å, Alternative crystal structure of mouse Cryptochrome 2 in complex with TH301 compound
4I6E 2.7 Å, A vertebrate cryptochrome
4U8H 2.8 Å, Crystal Structure of Mammalian Period-Cryptochrome Complex
7D0N 2.8 Å, Crystal structure of mouse CRY2 apo form

Browse structure collections

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