8JAU: CRL2APPBP2

Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer). Determined by electron microscopy at 3.22 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.22 Å
Organism: Homo sapiens
Chains: 10
Atoms: 17,064
Mol. weight: 359.42 kDa
Ligands: ZN
Released: 18 Oct 2023

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

Secondary structure: helices and β-sheets

8JAU contains 124 α-helices and 25 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	10-12	3
α-helix	13-23	11
α-helix	32-34	3
α-helix	37-50	14
α-helix	53-60	8
α-helix	63-69	7
α-helix	76-89	14
α-helix	93-108	16
α-helix	113-132	20
α-helix	136-151	16
α-helix	156-172	17
α-helix	179-198	20
α-helix	206-218	13
α-helix	222-233	12
α-helix	242-258	17
α-helix	262-279	18
α-helix	285-299	15
α-helix	304-321	18
α-helix	327-343	17
α-helix	352-367	16
α-helix	373-392	20
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	488-506	19
α-helix	511-513	3
α-helix	514-527	14
α-helix	530-550	21
α-helix	556-560	5
α-helix	567-576	10

Chain B: 33 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	13-23	11
α-helix	26-28	3
α-helix	30-33	4
α-helix	37-49	13
α-helix	53-60	8
α-helix	63-69	7
α-helix	76-89	14
α-helix	93-106	14
α-helix	113-132	20
α-helix	136-150	15
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	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	352-367	16
α-helix	373-392	20
α-helix	397-420	24
α-helix	426-441	16
α-helix	445-462	18
α-helix	468-479	12
α-helix	480-484	5
α-helix	490-505	16
α-helix	507-509	3
α-helix	512-527	16
α-helix	530-549	20
α-helix	570-576	7

Chain C: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	2
β-strand	12	1	3
β-strand	13-18	6	2
β-strand	23	1	4
α-helix	24-29	6
α-helix	39-41	3
β-strand	43-45	3	5
β-strand	50-51	2	5
β-strand	56	1	4
α-helix	72	1
β-strand	73-75	3	2
β-strand	76-78	3	5
α-helix	99-101	3

Chain D: 6 helices, 3 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
α-helix	48-51	4
β-strand	58-61	4	3
α-helix	67-83	17
α-helix	89-93	5
α-helix	97-110	14

Chain E: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	10-25	16
α-helix	32-46	15
β-strand	49	1	1
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	158-171	14
α-helix	178-190	13
α-helix	201-206	6
α-helix	208-229	22
α-helix	232-253	22
α-helix	256-258	3
α-helix	259-263	5
α-helix	265-267	3
α-helix	268-272	5
α-helix	275-279	5

Chain G: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	6
β-strand	9	1	7
β-strand	12	1	7
β-strand	16-19	4	6
α-helix	24-35	12
α-helix	39-41	3
β-strand	45-46	2	6
β-strand	49-50	2	6
α-helix	64-66	3
α-helix	72	1
β-strand	73-76	4	6
α-helix	86-88	3
α-helix	90-92	3

Chain H: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	8
β-strand	28	1	7
β-strand	30-32	3	8
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	8
α-helix	67-82	16
α-helix	91-93	3
α-helix	100-109	10

Chain I: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	10-24	15
α-helix	25-27	3
α-helix	32-46	15
α-helix	54-77	24
α-helix	83-104	22
α-helix	106-111	6
α-helix	139-147	9
α-helix	148-152	5
α-helix	156-170	15
α-helix	178-186	9
α-helix	192-194	3
α-helix	201-202	2
α-helix	203-208	6
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	275-288	14
α-helix	291-297	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloid protein-binding protein 2	A, B	protein	585	Homo sapiens	Q92624 (AlphaFold model)
Cullin-2	E, I	protein	745	Homo sapiens	Q13617 (AlphaFold model)
Elongin-B	C, G	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	D, H	protein	96	Homo sapiens	Q15369 (AlphaFold model)
MRPL28 C-degron	F, S	protein	16	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8JAU_1 Amyloid protein-binding protein 2 (chains A, B)
MAAVELEWIPETLYNTAISAVVDNYIRSRRDIRSLPENIQFDVYYKLYQQGRLCQLGSEF
CELEVFAKVLRALDKRHLLHHCFQALMDHGVKVASVLAYSFSRRCSYIAESDAAVKEKAI
QVGFVLGGFLSDAGWYSDAEKVFLSCLQLCTLHDEMLHWFRAVECCVRLLHVRNGNCKYH
LGEETFKLAQTYMDKLSKHGQQANKAALYGELCALLFAKSHYDEAYKWCIEAMKEITAGL
PVKVVVDVLRQASKACVVKREFKKAEQLIKHAVYLARDHFGSKHPKYSDTLLDYGFYLLN
VDNICQSVAIYQAALDIRQSVFGGKNIHVATAHEDLAYSSYVHQYSSGKFDNALFHAERA
IGIITHILPEDHLLLASSKRVKALILEEIAIDCHNKETEQRLLQEAHDLHLSSLQLAKKA
FGEFNVQTAKHYGNLGRLYQSMRKFKEAEEMHIKAIQIKEQLLGQEDYEVALSVGHLASL
YNYDMNQYENAEKLYLRSIAIGKKLFGEGYSGLEYDYRGLIKLYNSIGNYEKVFEYHNVL
SNWNRLRDRQYSVTDALEDVSTSPQSTEEVVQSFLISQNVEGPSC

Sequence of entity 2 (E, I), FASTA

>8JAU_2 Cullin-2 (chains E, I)
TSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA

Sequence of entity 3 (C, G), FASTA

>8JAU_3 Elongin-B (chains C, G)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 4 (D, H), FASTA

>8JAU_4 Elongin-C (chains D, H)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 5 (F, S), FASTA

>8JAU_5 MRPL28 C-degron (chains F, S)
QALSEPAVVQKRASGQ

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:

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)
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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