6KP3: Sendai virus Y3/ALIX-BRO1 domain complex

Structure of sendai virus Y3/ALIX-BRO1 domain complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 19 Aug 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Murine respirovirus
Chains: 2
Atoms: 3,900
Mol. weight: 56.36 kDa
Released: 19 Aug 2020

Explore 6KP3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KP3 contains 22 α-helices and 3 β-strands across 2 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: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	11-12	2	1
α-helix	18-28	11
α-helix	33-54	22
α-helix	62-78	17
β-strand	93-96	4	1
β-strand	110-113	4	1
α-helix	116-136	21
α-helix	143-166	24
α-helix	174-176	3
α-helix	181-205	25
α-helix	210-233	24
α-helix	241-266	26
α-helix	270-290	21
α-helix	298-314	17
α-helix	315-319	5
α-helix	326-328	3

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	95-109	15
α-helix	111-126	16
α-helix	128-129	2
α-helix	131-138	8
α-helix	141-160	20
α-helix	171-177	7
α-helix	178-181	4
α-helix	185-202	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 6-interacting protein	A	protein	372	Homo sapiens	Q8WUM4 (AlphaFold model)
C' protein	B	protein	119	Murine respirovirus	P04862

Sequence of entity 1 (A), FASTA

>6KP3_1 Programmed cell death 6-interacting protein (chains A)
MNHKVHHHHHHHHMATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELS
KLRRAAVGRPLDKHEGALETLLRYYDQICSIEPKFPFSENQICLTFTWKDAFDKGSLFGG
SVKLALASLGYEKSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKETV
LSALSREPTVDISPDTVGTLSLIMLAQAQEVFFLKATRDKMKDAIIAKLANQAADYFGDA
FKQCQYKDTLPKEVFPVLAAKHCIMQANAEYHQSILAKQQKKFGEEIARLQHAAELIKTV
ASRYDEYVNVKDFSDKINRALAAAKKDNDFIYHDRVPDLKDLDPIGKATLVKSTPVNVPI
SQKFTDLFEKMV

Sequence of entity 2 (B), FASTA

>6KP3_2 C' protein (chains B)
MNHKVHHHHHHHHMLETLINKIYTGPLGEELVQTLYLRIWAMEETPESLKILQMREDIRD
QVLKMKTERWLRTLIRGEKTKLKDFQKRYEEVHPYLMKEKVEQVIMEEAWSLAAHIVQE

Primary citation

Structural Insight into the Interaction of Sendai Virus C Protein with Alix To Stimulate Viral Budding. Oda, K., Matoba, Y., Sugiyama, M. et al. J Virol (2021):JVI0081521-JVI0081521. DOI 10.1128/JVI.00815-21 · PubMed

Other PDB entries of the same protein (UniProt Q8WUM4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WA1 1.87 Å, CHMP4C A232T in complex with ALIX BRO1
5V3R 1.91 Å, CHMP4C in complex with ALIX BRO1
3E1R 2.0 Å, Midbody targeting of the ESCRT machinery by a non-canonical coiled-coil in CEP55
3C3R 2.02 Å, ALIX BRO1 CHMP4C complex
3C3Q 2.1 Å, ALIX Bro1-domain:CHMIP4B co-crystal structure
3C3O 2.15 Å, ALIX Bro1-domain:CHMIP4A co-crystal structure
2ZNE 2.2 Å, Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide
2XS1 2.3 Å, Crystal Structure of ALIX in complex with the SIVmac239 PYKEVTEDL Late Domain
2XS8 2.5 Å, Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain
2OEW 2.55 Å, Structure of ALIX/AIP1 Bro1 Domain
2R05 2.55 Å, Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain
2OEX 2.58 Å, Structure of ALIX/AIP1 V Domain

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