5VK2: Antibody-mediated neutralization of Lassa virus
Structural basis for antibody-mediated neutralization of Lassa virus. Determined by X-ray diffraction at 3.2 Å resolution. Released 31 May 2017.
- Method
- X-ray diffraction
- Resolution
- 3.2 Å
- Organisms
- Lassa virus, Lassa virus (strain Mouse/Sierra Leone/Josiah/1976), Homo sapiens
- Chains
- 12
- Atoms
- 18,672
- Mol. weight
- 299.8 kDa
- Ligands
- NAG
- Released
- 31 May 2017
Explore 5VK2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5VK2 contains 86 α-helices and 196 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: 10 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 264-268 | 5 | |
| β-strand | 278-280 | 3 | 4 |
| β-strand | 285 | 1 | 2 |
| β-strand | 291-293 | 3 | 4 |
| α-helix | 295-298 | 4 | |
| α-helix | 300-303 | 4 | |
| α-helix | 308-325 | 18 | |
| α-helix | 334-344 | 11 | |
| α-helix | 347-358 | 12 | |
| β-strand | 363 | 1 | 5 |
| β-strand | 368-374 | 7 | 1 |
| β-strand | 380 | 1 | 1 |
| α-helix | 381-383 | 3 | |
| β-strand | 384-385 | 2 | 1 |
| β-strand | 388 | 1 | 5 |
| β-strand | 393 | 1 | 5 |
| α-helix | 394-395 | 2 | |
| α-helix | 396-398 | 3 | |
| α-helix | 400-415 | 16 | |
Chain A: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-62 | 2 | 1 |
| β-strand | 66-72 | 7 | 1 |
| β-strand | 73 | 1 | 2 |
| α-helix | 75-78 | 4 | |
| β-strand | 84-87 | 4 | 3 |
| β-strand | 92-97 | 6 | 3 |
| β-strand | 101-108 | 8 | 3 |
| α-helix | 120-125 | 6 | |
| α-helix | 131-143 | 13 | |
| α-helix | 150-152 | 3 | |
| β-strand | 153-155 | 3 | 3 |
| α-helix | 158-160 | 3 | |
| β-strand | 163-167 | 5 | 3 |
| α-helix | 183-194 | 12 | |
| α-helix | 200-203 | 4 | |
| β-strand | 219-226 | 8 | 3 |
| β-strand | 237 | 1 | 3 |
| α-helix | 239-246 | 8 | |
Chain b: 11 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 264-269 | 6 | |
| β-strand | 278-280 | 3 | 9 |
| β-strand | 285 | 1 | 7 |
| β-strand | 291-293 | 3 | 9 |
| α-helix | 295-298 | 4 | |
| α-helix | 300-303 | 4 | |
| α-helix | 308-325 | 18 | |
| α-helix | 327-329 | 3 | |
| α-helix | 335-344 | 10 | |
| α-helix | 347-358 | 12 | |
| β-strand | 363 | 1 | 10 |
| β-strand | 368-374 | 7 | 6 |
| β-strand | 380 | 1 | 6 |
| α-helix | 381-383 | 3 | |
| β-strand | 384-385 | 2 | 6 |
| β-strand | 388 | 1 | 10 |
| β-strand | 393 | 1 | 10 |
| α-helix | 394-395 | 2 | |
| α-helix | 396-398 | 3 | |
| α-helix | 400-415 | 16 | |
Chain B: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-62 | 2 | 6 |
| β-strand | 66-72 | 7 | 6 |
| β-strand | 73 | 1 | 7 |
| α-helix | 75-78 | 4 | |
| β-strand | 84-87 | 4 | 8 |
| β-strand | 92-97 | 6 | 8 |
| β-strand | 101-108 | 8 | 8 |
| α-helix | 120-125 | 6 | |
| α-helix | 131-143 | 13 | |
| β-strand | 153-155 | 3 | 8 |
| α-helix | 158-160 | 3 | |
| β-strand | 163-167 | 5 | 8 |
| α-helix | 183-194 | 12 | |
| α-helix | 200-203 | 4 | |
| β-strand | 219-226 | 8 | 8 |
| β-strand | 237 | 1 | 8 |
| α-helix | 239-246 | 8 | |
Chain c: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 278-280 | 3 | 14 |
| β-strand | 285 | 1 | 12 |
| β-strand | 291-293 | 3 | 14 |
| α-helix | 295-298 | 4 | |
| α-helix | 300-303 | 4 | |
| α-helix | 308-325 | 18 | |
| α-helix | 334-340 | 7 | |
| α-helix | 347-358 | 12 | |
| β-strand | 363 | 1 | 15 |
| β-strand | 368-374 | 7 | 11 |
| β-strand | 380 | 1 | 11 |
| α-helix | 381-383 | 3 | |
| β-strand | 384-385 | 2 | 11 |
| β-strand | 388 | 1 | 15 |
| β-strand | 393 | 1 | 15 |
| α-helix | 394-395 | 2 | |
| α-helix | 396-398 | 3 | |
| α-helix | 400-417 | 18 | |
Chain C: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-62 | 2 | 11 |
| β-strand | 66-72 | 7 | 11 |
| β-strand | 73 | 1 | 12 |
| α-helix | 75-78 | 4 | |
| β-strand | 84-87 | 4 | 13 |
| β-strand | 92-96 | 5 | 13 |
| β-strand | 101-108 | 8 | 13 |
| α-helix | 120-125 | 6 | |
| α-helix | 131-142 | 12 | |
| α-helix | 150-152 | 3 | |
| β-strand | 153-155 | 3 | 13 |
| α-helix | 158-160 | 3 | |
| β-strand | 163-167 | 5 | 13 |
| α-helix | 183-194 | 12 | |
| α-helix | 200-203 | 4 | |
| β-strand | 219-226 | 8 | 13 |
| β-strand | 237 | 1 | 13 |
| α-helix | 239-246 | 8 | |
Chain D: 5 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 16 |
| β-strand | 11-14 | 4 | 17 |
| β-strand | 19-26 | 8 | 16 |
| α-helix | 30-32 | 3 | |
| β-strand | 34-40 | 7 | 17 |
| β-strand | 46-52 | 7 | 17 |
| β-strand | 60-62 | 3 | 17 |
| β-strand | 70-75 | 6 | 16 |
| β-strand | 80-85 | 6 | 16 |
| β-strand | 94-102 | 9 | 17 |
| β-strand | 109-114 | 6 | 17 |
| β-strand | 118-123 | 6 | 17 |
| β-strand | 128 | 1 | 18 |
| β-strand | 131-135 | 5 | 19 |
| β-strand | 147-156 | 10 | 19 |
| β-strand | 157 | 1 | 18 |
| β-strand | 162-165 | 4 | 20 |
| α-helix | 166-168 | 3 | |
| β-strand | 170 | 1 | 20 |
| β-strand | 174-176 | 3 | 19 |
| α-helix | 177-179 | 3 | |
| β-strand | 180-181 | 2 | 19 |
| β-strand | 187-195 | 9 | 19 |
| α-helix | 199-202 | 4 | |
| β-strand | 205-211 | 7 | 20 |
| α-helix | 212-214 | 3 | |
| β-strand | 216-222 | 7 | 20 |
Chain E: 6 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 21 |
| β-strand | 6 | 1 | 22 |
| β-strand | 10-13 | 4 | 23 |
| β-strand | 19-24 | 6 | 22 |
| β-strand | 37-41 | 5 | 23 |
| β-strand | 48-52 | 5 | 23 |
| β-strand | 56-57 | 2 | 23 |
| α-helix | 58 | 1 | |
| β-strand | 65-70 | 6 | 22 |
| β-strand | 73-78 | 6 | 22 |
| α-helix | 83-85 | 3 | |
| β-strand | 87-93 | 7 | 23 |
| β-strand | 101-102 | 2 | 23 |
| β-strand | 103 | 1 | 21 |
| β-strand | 106-110 | 5 | 23 |
| β-strand | 116 | 1 | 24 |
| β-strand | 119-123 | 5 | 25 |
| α-helix | 124-126 | 3 | |
| α-helix | 127-130 | 4 | |
| β-strand | 135-144 | 10 | 25 |
| β-strand | 145 | 1 | 24 |
| β-strand | 150-155 | 6 | 26 |
| β-strand | 158-160 | 3 | 26 |
| β-strand | 164-166 | 3 | 25 |
| α-helix | 167-169 | 3 | |
| β-strand | 170-171 | 2 | 25 |
| β-strand | 177-185 | 9 | 25 |
| α-helix | 187-191 | 5 | |
| β-strand | 196-202 | 7 | 26 |
| β-strand | 205-211 | 7 | 26 |
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 |
|---|
| Pre-glycoprotein polyprotein GP complex | A, B, C | protein | 259 | Lassa virus | P08669 (AlphaFold model) |
| Pre-glycoprotein polyprotein GP complex | a, b, c | protein | 164 | Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) | P08669 (AlphaFold model) |
| Fab 37.7H heavy chain | D, F, H | protein | 229 | Homo sapiens | |
| Fab 37.7H light chain | E, G, L | protein | 217 | Homo sapiens | |
Sequence of entity 1 (A, B, C), FASTA
>5VK2_1 Pre-glycoprotein polyprotein GP complex (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRRR
Sequence of entity 2 (a, b, c), FASTA
>5VK2_2 Pre-glycoprotein polyprotein GP complex (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAPAQTSIQLINKAVNALINDQLIMKNHLRDIMCIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQ
Sequence of entity 3 (D, F, H), FASTA
>5VK2_3 Fab 37.7H heavy chain (chains D, F, H)
DEVQLVQSGGGLVKAGGSLRLSCAASGFTFSTYSMNWIRQAPGKGLEWVASISSRSGSHI
NYVDSVKGRFTISRDNARDLLYLQMNSLRVDDSALYYCARDRRSGTSPLPLDVWGQGTTV
TVFSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK
Sequence of entity 4 (E, G, L), FASTA
>5VK2_4 Fab 37.7H light chain (chains E, G, L)
DQSALTQPASVSGSPGQSITISCTGTGSDIGGYNFVSWYQQYPGKAPKLIIYEVRIRASG
VSNRFSGSKSGNTASLTISGLQAEDEADYYCNSYSIHSPWVFGGGTKLTVLRQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 11 |
Primary citation
Structural basis for antibody-mediated neutralization of Lassa virus. Hastie, K.M., Zandonatti, M.A., Kleinfelter, L.M. et al. Science (2017) 356:923-928. DOI 10.1126/science.aam7260 · 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
- 4ZJF 2.6 Å, Crystal structure of GP1 - the receptor binding domain of Lassa virus
- 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…
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