8JAR: CRL2APPBP2

Structure of CRL2APPBP2 bound with RxxGPAA degron (dimer). Determined by electron microscopy at 3.3 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 10
Atoms: 16,841
Mol. weight: 358.76 kDa
Ligands: ZN
Released: 18 Oct 2023

Explore 8JAR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JAR contains 130 α-helices and 31 β-strands across 8 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: 32 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	13-23	11
α-helix	26-28	3
α-helix	29-32	4
α-helix	37-49	13
α-helix	53-60	8
α-helix	63-70	8
α-helix	76-89	14
α-helix	93-108	16
α-helix	113-133	21
α-helix	136-152	17
α-helix	156-172	17
α-helix	179-197	19
α-helix	206-218	13
α-helix	222-234	13
α-helix	242-258	17
α-helix	262-275	14
α-helix	276-280	5
α-helix	285-299	15
α-helix	304-321	18
α-helix	327-343	17
α-helix	351-367	17
α-helix	373-390	18
α-helix	396-420	25
α-helix	426-441	16
α-helix	445-462	18
α-helix	468-479	12
α-helix	480-485	6
α-helix	488-506	19
α-helix	512-525	14
α-helix	530-550	21
α-helix	567-576	10

Chain B: 35 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	13-22	10
α-helix	32-34	3
α-helix	37-49	13
α-helix	53-60	8
α-helix	63-69	7
α-helix	76-89	14
α-helix	93-108	16
α-helix	113-133	21
α-helix	136-150	15
α-helix	156-174	19
α-helix	179-198	20
α-helix	202-204	3
α-helix	206-218	13
α-helix	222-234	13
α-helix	242-257	16
α-helix	262-275	14
α-helix	276-280	5
α-helix	285-300	16
α-helix	304-321	18
α-helix	327-343	17
α-helix	352-359	8
α-helix	361-367	7
α-helix	373-392	20
α-helix	397-420	24
α-helix	426-441	16
α-helix	445-461	17
α-helix	468-480	13
α-helix	481-485	5
α-helix	488-506	19
α-helix	513-527	15
α-helix	530-548	19
α-helix	553-555	3
α-helix	556-559	4
α-helix	570-576	7

Chain C: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	5-7	3	2
β-strand	12-14	3	2
β-strand	17-18	2	1
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-45	4	4
β-strand	50	1	4
β-strand	56	1	3
α-helix	57-60	4
α-helix	72	1
β-strand	73-75	3	2
β-strand	76-79	4	4
α-helix	86-88	3
α-helix	91-96	6
α-helix	99-101	3

Chain D: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	2
β-strand	28-32	5	2
α-helix	33-36	4
α-helix	40-45	6
α-helix	49-51	3
β-strand	58-61	4	2
α-helix	67-82	16
α-helix	91-93	3
α-helix	100-110	11

Chain E: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	10-25	16
α-helix	32-46	15
α-helix	54-78	25
α-helix	83-104	22
α-helix	106-108	3
α-helix	109-113	5
α-helix	139-147	9
α-helix	148-152	5
α-helix	158-172	15
α-helix	178-190	13
α-helix	191-193	3
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-228	20
α-helix	235-252	18
α-helix	256-258	3
α-helix	259-266	8
α-helix	267-271	5
α-helix	275-279	5

Chain G: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	9	1	6
β-strand	12	1	6
β-strand	15-18	4	5
β-strand	23	1	7
α-helix	24-35	12
α-helix	39-41	3
β-strand	45-46	2	8
β-strand	49-50	2	8
α-helix	51-52	2
β-strand	56	1	7
β-strand	68	1	9
β-strand	71	1	9
α-helix	72	1
β-strand	73	1	5
α-helix	74	1
β-strand	75-76	2	8
β-strand	80-81	2	10
β-strand	84-85	2	10
α-helix	86-88	3

Chain H: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	11
β-strand	28	1	11
β-strand	31	1	11
α-helix	33-36	4
α-helix	40-46	7
α-helix	54-56	3
β-strand	57-61	5	11
α-helix	67-82	16
α-helix	91-93	3
α-helix	100-108	9

Chain I: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	10-24	15
α-helix	25-27	3
α-helix	32-46	15
α-helix	54-78	25
α-helix	83-104	22
α-helix	106-108	3
α-helix	109-113	5
α-helix	139-147	9
α-helix	148-152	5
α-helix	156-170	15
α-helix	178-190	13
α-helix	191-194	4
α-helix	201-203	3
α-helix	204-208	5
α-helix	209-217	9
α-helix	219-225	7
α-helix	235-253	19
α-helix	256-258	3
α-helix	259-268	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloid protein-binding protein 2	A, B	protein	579	Homo sapiens	Q92624 (AlphaFold model)
Elongin-B	C, G	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	D, H	protein	96	Homo sapiens	Q15369 (AlphaFold model)
XP_211896+AA C-degron	F, S	protein	18	Homo sapiens
Cullin-2	E, I	protein	745	Homo sapiens	Q13617 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8JAR_1 Amyloid protein-binding protein 2 (chains A, B)
MAAVELEWIPETLYNTAISAVVDNYIRSRRDIRSLPENIQFDVYYKLYQQGRLCQLGSEF
CELEVFAKVLRALDKRHLLHHCFQALMDHGVKVASVLAYSFSRRCSYIAESDAAVKEKAI
QVGFVLGGFLSDAGWYSDAEKVFLSCLQLCTLHDEMLHWFRAVECCVRLLHVRNGNCKYH
LGEETFKLAQTYMDKLSKHGQQANKAALYGELCALLFAKSHYDEAYKWCIEAMKEITAGL
PVKVVVDVLRQASKACVVKREFKKAEQLIKHAVYLARDHFGSKHPKYSDTLLDYGFYLLN
VDNICQSVAIYQAALDIRQSVFGGKNIHVATAHEDLAYSSYVHQYSSGKFDNALFHAERA
IGIITHILPEDHLLLASSKRVKALILEEIAIDCHNKETEQRLLQEAHDLHLSSLQLAKKA
FGEFNVQTAKHYGNLGRLYQSMRKFKEAEEMHIKAIQIKEQLLGQEDYEVALSVGHLASL
YNYDMNQYENAEKLYLRSIAIGKKLFGEGYSGLEYDYRGLIKLYNSIGNYEKVFEYHNVL
SNWNRLRDRQYSVTDALEDVSTSPQSTEEVVQSFLISQN

Sequence of entity 2 (C, G), FASTA

>8JAR_2 Elongin-B (chains C, G)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (D, H), FASTA

>8JAR_3 Elongin-C (chains D, H)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (F, S), FASTA

>8JAR_4 XP_211896+AA C-degron (chains F, S)
TVPTLTRGRLTRNKGPAA

Sequence of entity 5 (E, I), FASTA

>8JAR_5 Cullin-2 (chains E, I)
TSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Molecular basis for C-degron recognition by CRL2 APPBP2 ubiquitin ligase. Zhao, S., Olmayev-Yaakobov, D., Ru, W. et al. Proc Natl Acad Sci U S A (2023) 120:e2308870120-e2308870120. DOI 10.1073/pnas.2308870120 · PubMed

Other PDB entries of the same protein (UniProt Q92624 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JAU 3.22 Å, Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer)
8JAQ 3.26 Å, Structure of CRL2APPBP2 bound with RxxGP degron (tetramer)
8JAL 3.3 Å, Structure of CRL2APPBP2 bound with RxxGP degron (dimer)
8JAV 3.44 Å, Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer)
8JAS 3.54 Å, Structure of CRL2APPBP2 bound with RxxGPAA degron (tetramer)

Browse structure collections

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