3VDX: PDB entry 3VDX

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Streptomyces aureofaciens, Influenza A virus
Chains: 3
Atoms: 10,149
Mol. weight: 150.79 kDa
Released: 20 Jun 2012

Explore 3VDX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VDX contains 73 α-helices and 43 β-strands across 3 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: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	11-16	6	1
β-strand	17-20	4	2
β-strand	24-29	6	2
α-helix	36-39	4
α-helix	42-49	8
β-strand	51-56	6	2
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	2
α-helix	98-101	4
α-helix	102-111	10
β-strand	116-122	7	2
β-strand	130	1	3
β-strand	140	1	3
α-helix	142-154	13
α-helix	156-167	12
β-strand	174	1	4
β-strand	178	1	4
α-helix	180-191	12
α-helix	197-200	4
α-helix	201-204	4
β-strand	221-225	5	2
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	2
α-helix	264-294	31
α-helix	303-315	13
α-helix	322-330	9
α-helix	337-350	14
α-helix	362-368	7
α-helix	369-371	3
α-helix	379-386	8
α-helix	392-399	8
α-helix	404-416	13
α-helix	423-436	14

Chain B: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	5
β-strand	8	1	6
β-strand	11	1	6
β-strand	14-16	3	5
β-strand	17-21	5	7
β-strand	25-29	5	7
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	7
α-helix	57-58	2
α-helix	73-86	14
β-strand	92-97	6	7
α-helix	98-100	3
α-helix	101-107	7
β-strand	116-122	7	7
β-strand	130	1	8
β-strand	140	1	8
α-helix	142-154	13
α-helix	156-167	12
β-strand	174	1	9
β-strand	178	1	9
α-helix	180-191	12
α-helix	202-204	3
β-strand	221-225	5	7
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	7
α-helix	264-283	20
α-helix	287-297	11
α-helix	303-315	13
α-helix	322-328	7
α-helix	337-350	14
α-helix	362-366	5
α-helix	373-377	5
α-helix	379-386	8
α-helix	392-396	5
α-helix	404-413	10
α-helix	424-433	10

Chain C: 27 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	10
β-strand	8	1	11
β-strand	11	1	11
β-strand	14-16	3	10
β-strand	17-20	4	12
β-strand	25-29	5	12
α-helix	36-39	4
α-helix	42-49	8
β-strand	52-56	5	12
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	12
α-helix	100-111	12
β-strand	116-122	7	12
β-strand	130	1	13
β-strand	140	1	13
α-helix	142-154	13
α-helix	156-163	8
α-helix	165-168	4
α-helix	170-173	4
β-strand	174	1	14
β-strand	178	1	14
α-helix	180-191	12
α-helix	195-200	6
α-helix	201-204	4
α-helix	213-215	3
β-strand	220-225	6	12
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	12
α-helix	264-278	15
α-helix	280-283	4
α-helix	285-295	11
α-helix	299	1
α-helix	302-316	15
α-helix	322-330	9
α-helix	337-349	13
α-helix	361-364	4
α-helix	373-386	14
α-helix	392-398	7
α-helix	404-415	12
α-helix	423-436	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix…	A, B, C	protein	456	Streptomyces aureofaciens, Influenza A virus	P03485 (AlphaFold model), P29715 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3VDX_1 Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1 (chains A, B, C)
MPFITVGQENSTSIDLYYEDHGTGVPVVLIHGFPLSGHSWERQSAALLDAGYRVITYDRR
GFGQSSQPTTGYDYDTFAADLNTVLETLDLQDAVLVGFSMGTGEVARYVSSYGTARIAAV
AFLASLEPFLLKTDDNPDGAAPQEFFDGIVAAVKADRYAFYTGFFNDFYNLDENLGTRIS
EEAVRNSWNTAASGGFFAAAAAPTTWYTDFRADIPRIDVPALILHGTGDRTLPIENTARV
FHKALPSAEYVEVEGAPHGLLWTHAEEVNTALLAFLAKALEAQKQKLLTEVETYVLSIIP
SGPLKAEIAQRLEDVFAGKNTDLEVLMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQR
RRFVQNALNGNGDPNNMDKAVKLYRKLKREITFHGAKEISLSYSAGALASCMGLIYNRMG
AVTTEVAFGLVCATCEQIADSQHRSHRQLEHHHHHH

Primary citation

Structure of a 16-nm cage designed by using protein oligomers. Lai, Y.T., Cascio, D., Yeates, T.O. Science (2012) 336:1129-1129. DOI 10.1126/science.1219351 · PubMed

Other PDB entries of the same protein (UniProt P03485 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VLL 1.6 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5TEZ 1.7 Å, TCR F50 recgonizing M1-HLA-A2
5ISZ 2.06 Å, Crystal structure of LS01-TCR/M1-HLA-A*02 complex
1AA7 2.08 Å, Influenza virus matrix protein crystal structure at PH 4.0
5CQE 2.1 Å, 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from…
5EUO 2.1 Å, PF6-M1-HLA-A2
1EA3 2.3 Å, Influenza virus M1 protein
2VLR 2.3 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5JHD 2.46 Å, Crystal structure of LS10-TCR/M1-HLA-A*02 complex
1HHI 2.5 Å, The antigenic identity of peptide(slash)mhc complexes: a comparison of the conformation…
7JM3 3.4 Å, Full-length three-dimensional structure of the influenza A virus M1 protein and its…
4IQ4 3.5 Å, Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains,…

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