8SZK: PPP2R5A/HIV-1 Vif/CBFb/EloB/EloC complex

The cryo-EM structure of PPP2R5A/HIV-1 Vif/CBFb/EloB/EloC complex. Determined by electron microscopy at 3.58 Å resolution. Released 5 Jun 2024.

Method: Electron microscopy
Resolution: 3.58 Å
Organisms: Homo sapiens, Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Chains: 5
Atoms: 7,392
Mol. weight: 124.88 kDa
Released: 5 Jun 2024

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

Secondary structure: helices and β-sheets

8SZK contains 54 α-helices and 21 β-strands across 5 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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	12-17	6	1
α-helix	25-35	11
β-strand	46	1	2
β-strand	49	1	2
α-helix	57-60	4
β-strand	73-74	2	1
α-helix	91-94	4

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	3
β-strand	28-32	5	3
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-62	4	3
α-helix	67-82	16
α-helix	90-92	3
α-helix	101-110	10

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	16-19	4
β-strand	25-29	5	4
α-helix	37-49	13
β-strand	55-58	4	4
β-strand	64-70	7	4
β-strand	85-87	3	4
β-strand	94-103	10	4
β-strand	106-115	10	4
β-strand	120-127	8	4
α-helix	137-148	12

Chain D: 32 helices, 0 β-strands

Element	Residues	Length
α-helix	56-58	3
α-helix	67-77	11
α-helix	93-109	17
α-helix	117-119	3
α-helix	120-131	12
α-helix	135-138	4
α-helix	149-151	3
α-helix	156-170	15
α-helix	177-183	7
α-helix	186-194	9
α-helix	195-197	3
α-helix	201-217	17
α-helix	222-237	16
α-helix	246-257	12
α-helix	261	1
α-helix	264	1
α-helix	266-271	6
α-helix	272-276	5
α-helix	277-281	5
α-helix	285-300	16
α-helix	304-306	3
α-helix	307-316	10
α-helix	323-336	14
α-helix	342-345	4
α-helix	349-359	11
α-helix	365-372	8
α-helix	373-376	4
α-helix	379-386	8
α-helix	388-401	14
α-helix	402-404	3
α-helix	409-422	14
α-helix	427-448	22

Chain G: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-13	9	4
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-42	4	4
β-strand	51-59	9	4
β-strand	62-69	8	4
β-strand	83-91	9	4
β-strand	94-97	4	4
α-helix	100-107	8
α-helix	108-110	3
α-helix	119-125	7
α-helix	136-138	3
α-helix	145-153	9
α-helix	162-164	3
α-helix	166-169	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	A	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	B	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Core-binding factor subunit beta	C	protein	201	Homo sapiens	Q13951 (AlphaFold model)
Virion infectivity factor	G	protein	176	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	P12504
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform	D	protein	486	Homo sapiens	Q15172

Sequence of entity 1 (A), FASTA

>8SZK_1 Elongin-B (chains A)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 2 (B), FASTA

>8SZK_2 Elongin-C (chains B)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C), FASTA

>8SZK_3 Core-binding factor subunit beta (chains C)
MGSSHHHHHHSQDPMPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQN
ACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGV
CVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEA
RRQQDPSPGSNLGGGDDLKLR

Sequence of entity 4 (G), FASTA

>8SZK_4 Virion infectivity factor (chains G)
MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLG
DAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAI
RNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

Sequence of entity 5 (D), FASTA

>8SZK_5 Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform (chains D)
MSSSSPPAGAASAAISASEKVDGFTRKSVRKAQRQKRSQGSSQFRSQGSQAELHPLPQLK
DATSNEQQELFCQKLQQCCILFDFMDSVSDLKSKEIKRATLNELVEYVSTNRGVIVESAY
SDIVKMISANIFRTLPPSDNPDFDPEEDEPTLEASWPHIQLVYEFFLRFLESPDFQPSIA
KRYIDQKFVQQLLELFDSEDPRERDFLKTVLHRIYGKFLGLRAFIRKQINNIFLRFIYET
EHFNGVAELLEILGSIINGFALPLKAEHKQFLMKVLIPMHTAKGLALFHAQLAYCVVQFL
EKDTTLTEPVIRGLLKFWPKTCSQKEVMFLGEIEEILDVIEPTQFKKIEEPLFKQISKCV
SSSHFQVAERALYFWNNEYILSLIEENIDKILPIMFASLYKISKEHWNPTIVALVYNVLK
TLMEMNGKLFDDLTSSYKAERQREKKKELEREELWKKLEELKLKKALEKQNSAYNMHSIL
SNTSAE

Primary citation

Structural insights into PPP2R5A degradation by HIV-1 Vif. Hu, Y., Delviks-Frankenberry, K.A., Wu, C. et al. Nat Struct Mol Biol (2024) 31:1492-1501. DOI 10.1038/s41594-024-01314-6 · PubMed

Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex

Browse structure collections

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