8JAQ: CRL2APPBP2

Structure of CRL2APPBP2 bound with RxxGP degron (tetramer). Determined by electron microscopy at 3.26 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.26 Å
Organism: Homo sapiens
Chains: 22
Atoms: 39,233
Mol. weight: 741.46 kDa
Ligands: ZN
Released: 18 Oct 2023

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

Secondary structure: helices and β-sheets

8JAQ contains 254 α-helices and 87 β-strands across 18 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: 33 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	1
α-helix	10-12	3
α-helix	13-23	11
α-helix	26-28	3
α-helix	32-34	3
α-helix	37-49	13
α-helix	53-60	8
α-helix	63-69	7
α-helix	77-89	13
α-helix	93-108	16
α-helix	113-132	20
α-helix	136-152	17
α-helix	156-174	19
α-helix	179-181	3
α-helix	182-199	18
α-helix	206-218	13
α-helix	222-234	13
α-helix	242-258	17
α-helix	262-279	18
α-helix	285-299	15
α-helix	308-321	14
α-helix	327-343	17
α-helix	351-367	17
α-helix	374-391	18
α-helix	396-420	25
α-helix	426-442	17
α-helix	445-462	18
α-helix	468-480	13
α-helix	481-485	5
α-helix	488-505	18
α-helix	513-524	12
α-helix	530-549	20
α-helix	556-560	5
α-helix	567-577	11

Chain B: 32 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	13-23	11
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	136-151	16
α-helix	156-174	19
α-helix	179-198	20
α-helix	206-218	13
α-helix	222-233	12
α-helix	242-258	17
α-helix	264-275	12
α-helix	276-280	5
α-helix	285-300	16
α-helix	304-321	18
α-helix	327-343	17
α-helix	352-367	16
α-helix	374-391	18
α-helix	396-420	25
α-helix	426-441	16
α-helix	445-462	18
α-helix	468-480	13
α-helix	481-485	5
α-helix	488-505	18
α-helix	507-509	3
α-helix	512-524	13
α-helix	533-550	18
α-helix	570-576	7

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	2
β-strand	14-15	2	2
β-strand	23	1	3
α-helix	24-35	12
β-strand	43-46	4	2
β-strand	49-50	2	2
α-helix	51-52	2
β-strand	56	1	3
α-helix	57-59	3
β-strand	73-78	6	2
α-helix	90-92	3
α-helix	95-98	4

Chain D: 5 helices, 4 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	40-46	7
β-strand	59-61	3	2
α-helix	67-82	16
β-strand	86	1	1
α-helix	90-93	4
α-helix	101-110	10

Chain E: 12 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	106-111	6
α-helix	139-147	9
α-helix	148-152	5
α-helix	158-172	15
α-helix	175-177	3
α-helix	178-185	8
α-helix	187-190	4
α-helix	201-206	6

Chain G: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	8-9	2	5
β-strand	12-13	2	5
β-strand	16-18	3	4
α-helix	24-35	12
β-strand	43	1	6
α-helix	46-48	3
α-helix	72	1
β-strand	73-75	3	4
β-strand	78	1	6
β-strand	80-81	2	7
β-strand	84-85	2	7
α-helix	86-88	3

Chain H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	8
β-strand	20-22	3	9
β-strand	28	1	9
β-strand	31	1	8
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	9
α-helix	67-82	16
α-helix	89-93	5
α-helix	100-109	10

Chain I: 31 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	32-46	15
α-helix	54-77	24
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	156-171	16
α-helix	178-190	13
α-helix	202-206	5
α-helix	208-229	22
α-helix	232-253	22
α-helix	256-258	3
α-helix	259-268	10
α-helix	275-280	6
α-helix	282-287	6
α-helix	291-303	13
α-helix	308-326	19
α-helix	335-356	22
α-helix	362-376	15
β-strand	379	1	10
β-strand	385	1	10
α-helix	387-399	13
α-helix	408-423	16
α-helix	428-444	17
α-helix	451-464	14
α-helix	471-481	11
α-helix	483-495	13
β-strand	508-513	6	11
α-helix	531-547	17
β-strand	551-555	5	11
β-strand	561-562	2	12
β-strand	574-576	3	13
β-strand	577-578	2	12
α-helix	579-590	12
β-strand	593-595	3	14
α-helix	596-602	7
α-helix	610-619	10
β-strand	623-624	2	14
β-strand	637-640	4	14
β-strand	650-652	3	13

10 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloid protein-binding protein 2	A, B, J, K	protein	578	Homo sapiens	Q92624 (AlphaFold model)
Cullin-2	E, I, L, U	protein	745	Homo sapiens	Q13617 (AlphaFold model)
Elongin-B	C, G, M, Q	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	D, H, N, T	protein	96	Homo sapiens	Q15369 (AlphaFold model)
XP_211896 C-degron	F, O, P, S	protein	16	Homo sapiens
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R, V	protein	108	Homo sapiens	P62877

Sequence of entity 1 (A, B, J, K), FASTA

>8JAQ_1 Amyloid protein-binding protein 2 (chains A, B, J, K)
MAAVELEWIPETLYNTAISAVVDNYIRSRRDIRSLPENIQFDVYYKLYQQGRLCQLGSEF
CELEVFAKVLRALDKRHLLHHCFQALMDHGVKVASVLAYSFSRRCSYIAESDAAVKEKAI
QVGFVLGGFLSDAGWYSDAEKVFLSCLQLCTLHDEMLHWFRAVECCVRLLHVRNGNCKYH
LGEETFKLAQTYMDKLSKHGQQANKAALYGELCALLFAKSHYDEAYKWCIEAMKEITAGL
PVKVVVDVLRQASKACVVKREFKKAEQLIKHAVYLARDHFGSKHPKYSDTLLDYGFYLLN
VDNICQSVAIYQAALDIRQSVFGGKNIHVATAHEDLAYSSYVHQYSSGKFDNALFHAERA
IGIITHILPEDHLLLASSKRVKALILEEIAIDCHNKETEQRLLQEAHDLHLSSLQLAKKA
FGEFNVQTAKHYGNLGRLYQSMRKFKEAEEMHIKAIQIKEQLLGQEDYEVALSVGHLASL
YNYDMNQYENAEKLYLRSIAIGKKLFGEGYSGLEYDYRGLIKLYNSIGNYEKVFEYHNVL
SNWNRLRDRQYSVTDALEDVSTSPQSTEEVVQSFLISQ

Sequence of entity 2 (E, I, L, U), FASTA

>8JAQ_2 Cullin-2 (chains E, I, L, U)
TSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA

Sequence of entity 3 (C, G, M, Q), FASTA

>8JAQ_3 Elongin-B (chains C, G, M, Q)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 4 (D, H, N, T), FASTA

>8JAQ_4 Elongin-C (chains D, H, N, T)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 5 (F, O, P, S), FASTA

>8JAQ_5 XP_211896 C-degron (chains F, O, P, S)
TVPTLTRGRLTRNKGP

Sequence of entity 6 (R, V), FASTA

>8JAQ_6 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R, V)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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)
8JAL 3.3 Å, Structure of CRL2APPBP2 bound with RxxGP degron (dimer)
8JAR 3.3 Å, Structure of CRL2APPBP2 bound with RxxGPAA 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)

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