4D9J: PDB entry 4D9J

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains. Determined by X-ray diffraction at 3.92 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 3.92 Å
Organisms: Streptomyces aureofaciens, Influenza A virus
Chains: 12
Atoms: 40,596
Mol. weight: 603.17 kDa
Released: 20 Jun 2012

Explore 4D9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D9J contains 290 α-helices and 180 β-strands across 12 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: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	8	1	2
β-strand	11	1	2
β-strand	14-16	3	1
β-strand	17-20	4	3
β-strand	25-29	5	3
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	3
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	3
α-helix	100-111	12
β-strand	116-122	7	3
β-strand	130	1	4
β-strand	140	1	4
α-helix	142-167	26
α-helix	170-173	4
β-strand	174	1	5
β-strand	178	1	5
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	3
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	3
α-helix	264-278	15
α-helix	280-294	15
α-helix	299	1
α-helix	302-316	15
α-helix	322-330	9
α-helix	337-350	14
α-helix	362-366	5
α-helix	373-387	15
α-helix	392-398	7
α-helix	404-415	12
α-helix	423-437	15

Chain B: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	6
β-strand	8	1	7
β-strand	11	1	7
β-strand	14-16	3	6
β-strand	17-20	4	8
β-strand	25-29	5	8
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	8
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	8
α-helix	100-111	12
β-strand	116-122	7	8
β-strand	130	1	9
β-strand	140	1	9
α-helix	142-154	13
α-helix	156-167	12
α-helix	170-173	4
β-strand	174	1	10
β-strand	178	1	10
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	8
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	8
α-helix	264-295	32
α-helix	299	1
α-helix	302-316	15
α-helix	322-330	9
α-helix	337-350	14
α-helix	362-366	5
α-helix	373-386	14
α-helix	392-398	7
α-helix	404-416	13
α-helix	423-436	14

Chain C: 25 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	11
β-strand	11-16	6	11
β-strand	17-20	4	12
β-strand	25-29	5	12
α-helix	36-39	4
α-helix	40-49	10
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	156-167	12
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	280-294	15
α-helix	299	1
α-helix	302-315	14
α-helix	322-330	9
α-helix	337-350	14
β-strand	359	1	15
α-helix	362-366	5
α-helix	373-386	14
α-helix	392-398	7
α-helix	404-415	12
α-helix	423-436	14

Chain D: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	16
β-strand	8	1	17
β-strand	11	1	17
β-strand	14-16	3	16
β-strand	17-20	4	18
β-strand	25-29	5	18
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	18
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	18
α-helix	100-111	12
β-strand	116-122	7	18
β-strand	130	1	19
β-strand	140	1	19
α-helix	142-167	26
α-helix	170-173	4
β-strand	174	1	20
β-strand	178	1	20
α-helix	180-191	12
α-helix	195-200	6
α-helix	201-204	4
α-helix	213-215	3
β-strand	221-225	5	18
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	18
α-helix	264-278	15
α-helix	280-294	15
α-helix	299	1
α-helix	302-315	14
α-helix	322-330	9
α-helix	337-350	14
α-helix	362-368	7
α-helix	373-387	15
α-helix	392-398	7
α-helix	404-415	12
α-helix	423-436	14

Chain E: 22 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	21
β-strand	11-16	6	21
β-strand	17-20	4	22
β-strand	25-29	5	22
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	22
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	22
α-helix	100-111	12
β-strand	116-122	7	22
β-strand	130	1	23
β-strand	140	1	23
α-helix	142-167	26
α-helix	170-173	4
β-strand	174	1	24
β-strand	178	1	24
α-helix	180-191	12
α-helix	195-200	6
α-helix	201-204	4
α-helix	213-215	3
β-strand	221-225	5	22
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	22
α-helix	264-294	31
α-helix	299	1
α-helix	302-316	15
α-helix	322-330	9
α-helix	337-350	14
α-helix	373-386	14
α-helix	392-398	7
α-helix	404-416	13
α-helix	423-436	14

Chain F: 24 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	25
β-strand	8	1	26
β-strand	11	1	26
β-strand	14-16	3	25
β-strand	17-20	4	27
β-strand	25-29	5	27
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	27
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	27
α-helix	100-111	12
β-strand	116-122	7	27
β-strand	130	1	28
β-strand	140	1	28
α-helix	142-167	26
α-helix	170-173	4
β-strand	174	1	29
β-strand	178	1	29
α-helix	180-191	12
α-helix	195-200	6
α-helix	201-204	4
α-helix	213-215	3
β-strand	221-225	5	27
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	27
α-helix	264-278	15
α-helix	280-294	15
α-helix	299	1
α-helix	302-315	14
α-helix	322-330	9
α-helix	337-350	14
β-strand	359	1	15
α-helix	362-366	5
α-helix	373-387	15
α-helix	392-398	7
α-helix	404-415	12
α-helix	423-436	14

Chain G: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	30
β-strand	8	1	31
β-strand	11	1	31
β-strand	14-16	3	30
β-strand	17-20	4	32
β-strand	25-29	5	32
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	32
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	32
α-helix	100-111	12
β-strand	116-122	7	32
β-strand	130	1	33
β-strand	140	1	33
α-helix	142-167	26
α-helix	170-173	4
β-strand	174	1	34
β-strand	178	1	34
α-helix	180-191	12
α-helix	195-200	6
α-helix	202-205	4
α-helix	213-215	3
β-strand	220-225	6	32
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	32
α-helix	264-278	15
α-helix	280-294	15
α-helix	299	1
α-helix	302-315	14
α-helix	322-330	9
α-helix	337-350	14
α-helix	362-366	5
α-helix	373-387	15
α-helix	392-398	7
α-helix	404-415	12
α-helix	423-436	14

Chain H: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	35
β-strand	8	1	36
β-strand	11	1	36
β-strand	14-16	3	35
β-strand	17-20	4	37
β-strand	25-29	5	37
α-helix	36-39	4
α-helix	40-49	10
β-strand	52-56	5	37
α-helix	57-58	2
α-helix	73-87	15
β-strand	92-97	6	37
α-helix	100-111	12
β-strand	116-122	7	37
β-strand	130	1	38
β-strand	140	1	38
α-helix	142-154	13
α-helix	156-167	12
α-helix	170-173	4
β-strand	174	1	39
β-strand	178	1	39
α-helix	180-191	12
α-helix	195-200	6
α-helix	201-204	4
α-helix	213-215	3
β-strand	221-225	5	37
α-helix	233-235	3
α-helix	237-243	7
β-strand	248-252	5	37
α-helix	264-294	31
α-helix	299	1
α-helix	302-316	15
α-helix	322-330	9
α-helix	337-350	14
β-strand	357	1	40
α-helix	362-366	5
α-helix	373-386	14
α-helix	392-398	7
α-helix	404-416	13
α-helix	422	1
α-helix	423-436	14

4 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
Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix…	A, B, C, D, E, F, G, H, I, J, K, L	protein	456	Streptomyces aureofaciens, Influenza A virus	P03485 (AlphaFold model), P29715 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>4D9J_1 Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1 (chains A, B, C, D, E, F, G, H, I, J, K, L)
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…
3VDX 3.0 Å, Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains
7JM3 3.4 Å, Full-length three-dimensional structure of the influenza A virus M1 protein and its…

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