8SZZ: Computationally Designed Nanocage O32-ZL4

CryoEM Structure of Computationally Designed Nanocage O32-ZL4. Determined by electron microscopy at 2.9 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: synthetic construct, Thermotoga maritima
Chains: 48
Atoms: 48,815
Mol. weight: 767.03 kDa
Released: 1 Nov 2023

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

Secondary structure: helices and β-sheets

8SZZ contains 329 α-helices and 240 β-strands across 48 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.

Chains 0, 1, 2, 3, P, q, r, R, s, S, t, T, u, v, V, w, W, x, X, y and z: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-34	33
α-helix	38-69	32

Chain a: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	41
α-helix	19-30	12
β-strand	36-40	5	41
α-helix	46-51	6
α-helix	54-58	5
β-strand	62-66	5	41
α-helix	72-80	9
β-strand	84-86	3	41
α-helix	92-99	8
β-strand	104-106	3	41
β-strand	108-109	2	42
α-helix	112-119	8
β-strand	125-128	4	42
α-helix	131-134	4
α-helix	137-140	4
β-strand	150-153	4	42
β-strand	154	1	41
α-helix	162-168	7
β-strand	173-175	3	41
α-helix	177-180	4
α-helix	186-198	13

Chain b: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	43
α-helix	19-32	14
β-strand	36-40	5	43
α-helix	46-52	7
α-helix	56-59	4
β-strand	62-66	5	43
α-helix	71-79	9
β-strand	84-86	3	43
α-helix	92-98	7
β-strand	104-106	3	43
β-strand	108-109	2	44
α-helix	112-120	9
β-strand	125-128	4	44
α-helix	131-134	4
α-helix	136-142	7
β-strand	150-153	4	44
β-strand	154	1	43
α-helix	162-167	6
β-strand	173-175	3	43
α-helix	177-180	4
α-helix	184-200	17

Chain c: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	45
α-helix	19-30	12
β-strand	36-40	5	45
α-helix	46-51	6
α-helix	54-59	6
β-strand	62-66	5	45
α-helix	71-80	10
β-strand	84-86	3	45
α-helix	92-99	8
β-strand	104-106	3	45
β-strand	108-109	2	46
α-helix	112-119	8
β-strand	125-128	4	46
α-helix	131-134	4
α-helix	136-141	6
β-strand	150-153	4	46
β-strand	154	1	45
α-helix	162-168	7
β-strand	173-175	3	45
α-helix	177-180	4
α-helix	186-198	13

Chain d: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	47
α-helix	19-32	14
β-strand	36-40	5	47
α-helix	46-51	6
α-helix	55-59	5
β-strand	62-66	5	47
α-helix	71-80	10
β-strand	84-86	3	47
α-helix	92-99	8
β-strand	104-106	3	47
β-strand	108-109	2	48
α-helix	112-121	10
β-strand	125-128	4	48
α-helix	131-134	4
α-helix	136-140	5
β-strand	150-153	4	48
β-strand	154	1	47
α-helix	162-167	6
β-strand	173-175	3	47
α-helix	177-180	4
α-helix	186-198	13

Chain e: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	1
α-helix	19-30	12
β-strand	36-40	5	1
α-helix	46-52	7
α-helix	54-57	4
β-strand	62-66	5	1
α-helix	71-80	10
β-strand	84-86	3	1
α-helix	93-96	4
β-strand	104-106	3	1
β-strand	108-109	2	2
α-helix	112-119	8
β-strand	125-128	4	2
α-helix	131-134	4
α-helix	136-142	7
β-strand	150-153	4	2
β-strand	154	1	1
α-helix	162-167	6
β-strand	173-175	3	1
α-helix	177-180	4
α-helix	186-198	13

Chains f and h: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	3
α-helix	19-32	14
β-strand	36-40	5	3
α-helix	46-52	7
α-helix	54-59	6
β-strand	62-66	5	3
α-helix	71-80	10
β-strand	84-86	3	3
α-helix	92-100	9
β-strand	104-106	3	3
β-strand	108-109	2	4
α-helix	112-121	10
β-strand	125-128	4	4
α-helix	131-134	4
α-helix	136-141	6
β-strand	150-153	4	4
β-strand	154	1	3
α-helix	162-168	7
β-strand	173-175	3	3
α-helix	177-180	4
α-helix	186-200	15

Chain g: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	10-14	5	5
α-helix	19-32	14
β-strand	36-40	5	5
α-helix	46-51	6
α-helix	56-59	4
β-strand	62-66	5	5
α-helix	71-79	9
β-strand	84-86	3	5
α-helix	92-100	9
β-strand	104-106	3	5
β-strand	108-109	2	6
α-helix	112-119	8
β-strand	125-128	4	6
α-helix	131-134	4
α-helix	136-141	6
β-strand	150-153	4	6
β-strand	154	1	5
α-helix	162-168	7
β-strand	173-175	3	5
α-helix	186-200	15

18 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
O32-ZL4 Component A	0, 1, 2, 3, P, Q, R, S, T, V, W, X, o, p, q, r, s, t, u, v, w, x, y, z	protein	76	synthetic construct
O32-ZL4 Component B	I, J, K, L, M, N, O, U, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n	protein	213	Thermotoga maritima	Q9WXS1 (AlphaFold model)

Sequence of entity 1 (0, 1, 2, 3, P, Q, R, S, T, V, W, X, o, p, q, r, s, t, u, v, w, x, y, z), FASTA

>8SZZ_1 O32-ZL4 Component A (chains 0, 1, 2, 3, P, Q, R, S, T, V, W, X, o, p, q, r, s, t, u, v, w, x, y, z)
MTDELLRLAKEQAELLKEIKILVELIAMLVKVIQKDPSDEALKALAELVRKLKELVEDME
RSMKEQLYIIKGSWSG

Sequence of entity 2 (I, J, K, L, M, N, O, U, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n), FASTA

>8SZZ_2 O32-ZL4 Component B (chains I, J, K, L, M, N, O, U, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n)
MKMEELFKKHKIVAVLRANDAQEAREKALAVFEGGVHLIEITFTVPNAAAVILLLSFLKE
KGAIIGAGTVTSEEQCALAVLSGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKA
MKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSA
LVKGTPDEVREKAKAFVEKIRGCTELEHHHHHH

Primary citation

Accurate computational design of three-dimensional protein crystals. Li, Z., Wang, S., Nattermann, U. et al. Nat Mater (2023) 22:1556-1563. DOI 10.1038/s41563-023-01683-1 · PubMed

Other PDB entries of the same protein (UniProt Q9WXS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WA3 1.9 Å, Mechanism of the Class I KDPG aldolase
9UAQ 2.29 Å, CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
1VLW 2.3 Å, Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate…
9UCL 2.43 Å, CryoEM structure of IgV domain of human Nectin-4 with Trimbody
9XOU 2.5 Å, CryoEM structure of LacY with Trimbody
9UBR 2.62 Å, CryoEM structure of human Galectin-10 with iTrimbody
8TVB 2.9 Å, Ghanaian virus fusion glycoprotein (GhV F)
8TYC 3.3 Å, Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1
8E01 3.4 Å, Structure of engineered nano-cage fusion protein
8JGC 3.44 Å, Cryo-EM structure of Mi3 fused with LOV2
8JGA 3.68 Å, Cryo-EM structure of Mi3 fused with FKBP
7B3Y 3.7 Å, Structure of a nanoparticle for a COVID-19 vaccine candidate

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