4ZJF: GP1 - the receptor binding domain of Lassa virus

Crystal structure of GP1 - the receptor binding domain of Lassa virus. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 May 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Lassa virus Josiah
Chains: 4
Atoms: 5,359
Mol. weight: 81.83 kDa
Ligands: NAG
Released: 27 May 2015

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

Secondary structure: helices and β-sheets

4ZJF contains 20 α-helices and 40 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.

Chain A: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	79	1	1
α-helix	81-83	3
β-strand	84	1	2
β-strand	91-95	5	3
β-strand	101-108	8	3
α-helix	123-139	17
β-strand	152-158	7	3
β-strand	161-167	7	3
α-helix	173-178	6
α-helix	183-194	12
β-strand	201-204	4	4
β-strand	211-214	4	4
β-strand	219-226	8	3
β-strand	232	1	2
α-helix	233-235	3

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	82-83	2
β-strand	84	1	5
β-strand	91-95	5	6
β-strand	102-108	7	6
α-helix	123-139	17
β-strand	152-158	7	6
β-strand	161-167	7	6
α-helix	173-178	6
α-helix	183-194	12
β-strand	198	1	7
β-strand	201-204	4	8
β-strand	211-214	4	8
β-strand	219-225	7	6
β-strand	232	1	5
α-helix	233-235	3

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	79	1	7
α-helix	81-82	2
β-strand	84	1	9
β-strand	91-95	5	10
β-strand	101-108	8	10
α-helix	123-139	17
β-strand	152-158	7	10
β-strand	161-167	7	10
α-helix	173-178	6
α-helix	183-194	12
β-strand	201-204	4	11
β-strand	211-214	4	11
β-strand	219-226	8	10
β-strand	232	1	9
α-helix	233-235	3

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	82-83	2
β-strand	84	1	12
β-strand	91-95	5	13
β-strand	102-108	7	13
α-helix	123-139	17
β-strand	152-158	7	13
β-strand	161-167	7	13
α-helix	173-178	6
α-helix	183-193	11
β-strand	198	1	1
β-strand	201-204	4	14
β-strand	211-214	4	14
β-strand	219-225	7	13
β-strand	232	1	12
α-helix	233-235	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein	A, B, C, D	protein	172	Lassa virus Josiah	P08669 (AlphaFold model)

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

>4ZJF_1 Glycoprotein (chains A, B, C, D)
SHHHHHHGGMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHK
KNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVAN
GVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Molecular Mechanism for LAMP1 Recognition by Lassa Virus. Cohen-Dvashi, H., Cohen, N., Israeli, H. et al. J Virol (2015) 89:7584-7592. DOI 10.1128/JVI.00651-15 · PubMed

Other PDB entries of the same protein (UniProt P08669 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MJ1 1.9 Å, Native tagless Lassa virus spike complex bound at pH 8.0
9MHE 2.01 Å, Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0
9MIV 2.02 Å, Native tagless Lassa virus spike complex pH 6.0
5OMI 2.56 Å, Crystal structure of GP2 from Lassa virus in a post fusion conformation
9MJ2 2.58 Å, Flag-tag Lassa virus spike complex at pH 6.0
7S8H 2.7 Å, Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F
9MIY 2.72 Å, Focused reconstruction of the transmembrane region of the Lassa virus spike complex
7UOV 2.75 Å, Native Lassa glycoprotein in complex with neutralizing antibodies 12.1F and 37.2D
7UOT 2.77 Å, Native Lassa glycoprotein in complex with neutralizing antibodies 8.9F and 37.2D
7TYV 2.8 Å, Structure of Lassa Virus glycoprotein (Josiah) bound to Fab 25.10C
8VCV 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…
8VE8 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…

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