8JAV: CRL2APPBP2

Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer). Determined by electron microscopy at 3.44 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.44 Å
Organism: Homo sapiens
Chains: 22
Atoms: 39,339
Mol. weight: 743.81 kDa
Ligands: ZN
Released: 18 Oct 2023

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

Secondary structure: helices and β-sheets

8JAV contains 256 α-helices and 90 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: 32 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	1
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	53-56	4
α-helix	63-66	4
α-helix	77-89	13
α-helix	93-108	16
α-helix	113-132	20
α-helix	136-151	16
α-helix	156-174	19
α-helix	179-198	20
α-helix	206-218	13
α-helix	222-235	14
α-helix	242-256	15
α-helix	262-279	18
α-helix	285-299	15
α-helix	304-321	18
α-helix	327-343	17
α-helix	351-367	17
α-helix	373-392	20
α-helix	396-420	25
α-helix	426-441	16
α-helix	445-463	19
α-helix	468-480	13
α-helix	481-485	5
α-helix	488-505	18
α-helix	511-527	17
α-helix	530-550	21
α-helix	556-559	4
α-helix	567-577	11

Chain B: 31 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	13-22	10
α-helix	25-32	8
α-helix	37-49	13
α-helix	57-60	4
α-helix	63-70	8
α-helix	77-89	13
α-helix	93-108	16
α-helix	113-133	21
α-helix	137-150	14
α-helix	156-174	19
α-helix	179-197	19
α-helix	206-218	13
α-helix	222-235	14
α-helix	242-258	17
α-helix	264-279	16
α-helix	285-299	15
α-helix	304-321	18
α-helix	327-343	17
α-helix	353-367	15
α-helix	373-392	20
α-helix	397-421	25
α-helix	426-441	16
α-helix	445-463	19
α-helix	468-480	13
α-helix	481-485	5
α-helix	488-505	18
α-helix	507-509	3
α-helix	512-527	16
α-helix	530-549	20
α-helix	570-576	7

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	2
β-strand	14	1	3
β-strand	16-18	3	2
α-helix	25-35	11
β-strand	43-46	4	2
β-strand	49-50	2	2
β-strand	68	1	4
β-strand	71	1	4
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	3
β-strand	28-32	5	3
α-helix	33-36	4
α-helix	40-45	6
β-strand	58-61	4	3
α-helix	67-82	16
β-strand	86	1	1
α-helix	90-93	4
α-helix	100-110	11

Chain E: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	10-25	16
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	163-172	10
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	5
β-strand	8-9	2	6
β-strand	12-13	2	6
β-strand	16-18	3	5
α-helix	24-35	12
β-strand	43	1	7
α-helix	46-48	3
α-helix	72	1
β-strand	73-75	3	5
β-strand	78	1	7
β-strand	80-81	2	8
β-strand	84-85	2	8
α-helix	86-88	3

Chain H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	9
β-strand	22	1	10
β-strand	28	1	10
β-strand	31	1	9
α-helix	33-36	4
α-helix	40-46	7
β-strand	61	1	10
α-helix	67-82	16
α-helix	90-94	5
α-helix	100-109	10

Chain I: 34 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	32-46	15
α-helix	55-77	23
α-helix	83-104	22
α-helix	106-108	3
α-helix	109-113	5
α-helix	139-150	12
α-helix	156-171	16
α-helix	178-186	9
α-helix	190-195	6
α-helix	199-201	3
α-helix	202-203	2
α-helix	204-208	5
α-helix	209-227	19
α-helix	232-253	22
α-helix	256-258	3
α-helix	259-267	9
α-helix	268-272	5
α-helix	275-286	12
α-helix	291-303	13
α-helix	308-326	19
α-helix	335-356	22
α-helix	362-376	15
α-helix	387-399	13
α-helix	408-423	16
α-helix	428-444	17
α-helix	451-464	14
α-helix	472-476	5
α-helix	480-495	16
β-strand	506-513	8	11
α-helix	534-547	14
β-strand	551-552	2	12
α-helix	557-559	3
β-strand	561-562	2	11
β-strand	574-576	3	13
β-strand	577	1	11
α-helix	579-590	12
β-strand	593-595	3	14
α-helix	596-603	8
α-helix	607-620	14
β-strand	623-625	3	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	585	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)
MRPL28 C-degron	F, O, P, S	protein	16	Homo sapiens	Q13084
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R, V	protein	108	Homo sapiens	P62877

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

>8JAV_1 Amyloid protein-binding protein 2 (chains A, B, J, K)
MAAVELEWIPETLYNTAISAVVDNYIRSRRDIRSLPENIQFDVYYKLYQQGRLCQLGSEF
CELEVFAKVLRALDKRHLLHHCFQALMDHGVKVASVLAYSFSRRCSYIAESDAAVKEKAI
QVGFVLGGFLSDAGWYSDAEKVFLSCLQLCTLHDEMLHWFRAVECCVRLLHVRNGNCKYH
LGEETFKLAQTYMDKLSKHGQQANKAALYGELCALLFAKSHYDEAYKWCIEAMKEITAGL
PVKVVVDVLRQASKACVVKREFKKAEQLIKHAVYLARDHFGSKHPKYSDTLLDYGFYLLN
VDNICQSVAIYQAALDIRQSVFGGKNIHVATAHEDLAYSSYVHQYSSGKFDNALFHAERA
IGIITHILPEDHLLLASSKRVKALILEEIAIDCHNKETEQRLLQEAHDLHLSSLQLAKKA
FGEFNVQTAKHYGNLGRLYQSMRKFKEAEEMHIKAIQIKEQLLGQEDYEVALSVGHLASL
YNYDMNQYENAEKLYLRSIAIGKKLFGEGYSGLEYDYRGLIKLYNSIGNYEKVFEYHNVL
SNWNRLRDRQYSVTDALEDVSTSPQSTEEVVQSFLISQNVEGPSC

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

>8JAV_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

>8JAV_3 Elongin-B (chains C, G, M, Q)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

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

>8JAV_4 Elongin-C (chains D, H, N, T)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

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

>8JAV_5 MRPL28 C-degron (chains F, O, P, S)
QALSEPAVVQKRASGQ

Sequence of entity 6 (R, V), FASTA

>8JAV_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)
8JAQ 3.26 Å, Structure of CRL2APPBP2 bound with RxxGP degron (tetramer)
8JAL 3.3 Å, Structure of CRL2APPBP2 bound with RxxGP degron (dimer)
8JAR 3.3 Å, Structure of CRL2APPBP2 bound with RxxGPAA degron (dimer)
8JAS 3.54 Å, Structure of CRL2APPBP2 bound with RxxGPAA degron (tetramer)

Browse structure collections

About this viewer

MolViewer shows 8JAV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.