6GH8: GP1 domain of Lujo virus

Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of neuropilin-2. Determined by X-ray diffraction at 2.44 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 2.44 Å
Organisms: Lujo mammarenavirus, Homo sapiens
Chains: 4
Atoms: 3,801
Mol. weight: 62.62 kDa
Ligands: CA, NAG
Released: 25 Jul 2018

Explore 6GH8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GH8 contains 15 α-helices and 38 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: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	2
β-strand	38-41	4	3
α-helix	48-50	3
β-strand	54-60	7	2
β-strand	68-72	5	3
β-strand	77	1	4
β-strand	78	1	5
β-strand	87-92	6	2
β-strand	99-104	6	2
β-strand	106	1	5
β-strand	113-114	2	3
β-strand	119-125	7	2
β-strand	134	1	4
β-strand	136-141	6	3

Chains B and D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	89-91	3	6
β-strand	96-102	7	6
α-helix	105-106	2
α-helix	108	1
β-strand	109-110	2	6
α-helix	111	1
α-helix	113-119	7
α-helix	121-134	14
β-strand	143-145	3	6
β-strand	152-158	7	6
α-helix	162-173	12
β-strand	183-190	8	6

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	7
β-strand	38-41	4	8
α-helix	48-50	3
β-strand	54-60	7	7
β-strand	68-72	5	8
β-strand	77	1	9
β-strand	78	1	10
β-strand	87-91	5	7
α-helix	99	1
β-strand	100-104	5	7
β-strand	106	1	10
β-strand	113-114	2	8
β-strand	119-125	7	7
β-strand	134	1	9
β-strand	136-141	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein	B, D	protein	139	Lujo mammarenavirus	C5ILC1 (AlphaFold model)
Neuropilin-2	A, C	protein	133	Homo sapiens	O60462 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>6GH8_1 Glycoprotein (chains B, D)
ADLGSHHHHHHGGMSLLSSIPMVSEQQHCIQHNHSSITFSLLTNKSDLEKCNFTRLQAVD
RVIFDLFREFHHRVGDFPVTSDLKCSHNTSYRVIEYEVTKESLPRLQEAVSTLFPDLHLS
EDRFLQIQAHDDKNCTGLH

Sequence of entity 2 (A, C), FASTA

>6GH8_2 Neuropilin-2 (chains A, C)
ADLGSPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKH
DCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIRFTSDYARQGAGFSLRYEI
FKTGSGTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Structural basis for receptor recognition by Lujo virus. Cohen-Dvashi, H., Kilimnik, I., Diskin, R. Nat Microbiol (2018) 3:1153-1160. DOI 10.1038/s41564-018-0224-5 · PubMed

Other PDB entries of the same protein (UniProt C5ILC1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P4T 2.96 Å, The spike complex of the Lujo Virus

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