1DYL: Nucleocapsid protein

9 Å resolution cryo-EM reconstruction structure of semliki forest virus (SFV) and fitting of the capsid protein structure in the EM density. Determined by electron microscopy at 9.0 Å resolution. Released 18 Aug 2000.

Method: Electron microscopy
Resolution: 9.0 Å
Organism: SEMLIKI FOREST VIRUS
Chains: 4
Atoms: 4,563
Mol. weight: 65.01 kDa
Released: 18 Aug 2000

Explore 1DYL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DYL contains 20 α-helices and 72 β-strands across 4 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 A and D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	121-125	5	1
β-strand	128-133	6	1
β-strand	135-136	2	2
β-strand	139-140	2	2
β-strand	143	1	3
β-strand	149-150	2	1
α-helix	153-156	4
β-strand	161-163	3	3
β-strand	168-170	3	3
β-strand	171-172	2	2
α-helix	173-174	2
α-helix	175-180	6
α-helix	181	1
β-strand	182	1	2
α-helix	183	1
β-strand	184	1	4
β-strand	191-195	5	4
β-strand	198-202	5	4
β-strand	207-210	4	4
β-strand	222-224	3	4
β-strand	230-240	11	4
β-strand	243-251	9	4
β-strand	256-259	4	4

Chain B: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	121-125	5	5
β-strand	128-133	6	5
β-strand	135-136	2	6
β-strand	139-140	2	6
β-strand	143	1	7
β-strand	149-150	2	5
α-helix	153-156	4
β-strand	161-163	3	7
β-strand	168-170	3	7
β-strand	171-172	2	6
α-helix	173-174	2
α-helix	175-180	6
α-helix	181	1
β-strand	182	1	6
α-helix	183	1
β-strand	184	1	8
β-strand	190	1	9
β-strand	191-195	5	8
β-strand	198-202	5	8
β-strand	207-210	4	8
β-strand	222-224	3	8
β-strand	230-240	11	8
β-strand	243-251	9	8
β-strand	256-259	4	8

Chain C: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	121-133	13	9
β-strand	135-136	2	10
β-strand	139-140	2	10
β-strand	143	1	11
β-strand	149-150	2	9
α-helix	153-156	4
β-strand	161-163	3	11
β-strand	168-170	3	11
β-strand	171-172	2	10
α-helix	173-174	2
α-helix	175-180	6
α-helix	181	1
β-strand	182	1	10
α-helix	183	1
β-strand	184	1	12
β-strand	191-195	5	12
β-strand	198-202	5	12
β-strand	207-210	4	12
β-strand	222-224	3	12
β-strand	230-240	11	12
β-strand	243-251	9	12
β-strand	256-259	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleocapsid protein	A, B, C, D	protein	149	SEMLIKI FOREST VIRUS	P03315 (AlphaFold model)

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

>1DYL_1 NUCLEOCAPSID PROTEIN (chains A, B, C, D)
CIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMR
SDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGA
NEGSRTALSVVTWNKDMVTRVTPEGSEEW

Primary citation

Cryo-Electron Microscopy Reveals the Functional Organization of an Enveloped Virus, Semliki Forest Virus. Mancini, E.J., Clarke, M., Gowen, B.E. et al. Mol Cell (2000) 5:255-266. DOI 10.1016/S1097-2765(00)80421-9 · PubMed

Other PDB entries of the same protein (UniProt P03315 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2V33 1.55 Å, High resolution crystal structure of domain III of E1 fusion glycoprotein of Semliki…
1I9W 3.0 Å, Crystal structure of the fusion glycoprotein E1 from semliki forest virus
1VCP 3.0 Å, Semliki forest virus capsid protein (crystal form I)
2ALA 3.0 Å, Crystal structure of the Semliki Forest Virus envelope protein E1 in its monomeric…
8IHP 3.0 Å, Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3
8YVY 3.02 Å, Semliki Forest virus virion
1VCQ 3.1 Å, Semliki forest virus capsid protein (crystal form II)
1RER 3.2 Å, Crystal structure of the homotrimer of fusion glycoprotein E1 from Semliki Forest Virus.
8YW1 3.44 Å, Semliki Forest virus viron in complex with VLDLR
8YVZ 3.45 Å, Semliki Forest virus viron
8X0K 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)
8X0L 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)

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