6C5V: Envelope glycoprotein H
An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus. Determined by electron microscopy at 4.8 Å resolution. Released 2 May 2018.
- Method
- Electron microscopy
- Resolution
- 4.8 Å
- Organisms
- Human herpesvirus 4, Homo sapiens
- Chains
- 5
- Atoms
- 10,649
- Mol. weight
- 167.51 kDa
- Ligands
- NAG
- Released
- 2 May 2018
Explore 6C5V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6C5V contains 64 α-helices and 89 β-strands across 5 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: 36 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-29 | 7 | 1 |
| β-strand | 32-38 | 7 | 1 |
| α-helix | 41-44 | 4 | |
| α-helix | 52-59 | 8 | |
| α-helix | 65-74 | 10 | |
| β-strand | 75 | 1 | 2 |
| α-helix | 93-96 | 4 | |
| α-helix | 99 | 1 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 104-106 | 3 | |
| β-strand | 119-122 | 4 | 3 |
| α-helix | 123-130 | 8 | |
| β-strand | 134-138 | 5 | 4 |
| β-strand | 148 | 1 | 5 |
| β-strand | 151-154 | 4 | 4 |
| β-strand | 156-162 | 7 | 6 |
| β-strand | 167-173 | 7 | 6 |
| β-strand | 177-185 | 9 | 6 |
| β-strand | 191-200 | 10 | 6 |
| α-helix | 201-203 | 3 | |
| α-helix | 204-206 | 3 | |
| β-strand | 207 | 1 | 5 |
| α-helix | 213-215 | 3 | |
| β-strand | 217-220 | 4 | 6 |
| β-strand | 224-229 | 6 | 6 |
| β-strand | 231 | 1 | 2 |
| α-helix | 232-238 | 7 | |
| α-helix | 246-255 | 10 | |
| α-helix | 258-274 | 17 | |
| α-helix | 285-306 | 22 | |
| β-strand | 312-314 | 3 | 3 |
| α-helix | 315-335 | 21 | |
| β-strand | 339-341 | 3 | 6 |
| α-helix | 346-356 | 11 | |
| α-helix | 361-366 | 6 | |
| α-helix | 369-382 | 14 | |
| α-helix | 384-386 | 3 | |
| α-helix | 392-404 | 13 | |
| α-helix | 408 | 1 | |
| α-helix | 415-431 | 17 | |
| α-helix | 440-452 | 13 | |
| α-helix | 456-468 | 13 | |
| α-helix | 471-474 | 4 | |
| α-helix | 477-480 | 4 | |
| β-strand | 483 | 1 | 7 |
| α-helix | 488-493 | 6 | |
| α-helix | 503-516 | 14 | |
| α-helix | 522-524 | 3 | |
| α-helix | 530-534 | 5 | |
| α-helix | 538-540 | 3 | |
| β-strand | 541-547 | 7 | 7 |
| β-strand | 550-555 | 6 | 7 |
| β-strand | 566-567 | 2 | 7 |
| α-helix | 575-576 | 2 | |
| β-strand | 578-583 | 6 | 7 |
| α-helix | 592 | 1 | |
| α-helix | 595-596 | 2 | |
| β-strand | 597 | 1 | 7 |
| α-helix | 598 | 1 | |
| β-strand | 601-602 | 2 | 8 |
| β-strand | 618-623 | 6 | 8 |
| β-strand | 627-633 | 7 | 8 |
| α-helix | 637-645 | 9 | |
| β-strand | 656-661 | 6 | 8 |
| β-strand | 667-670 | 4 | 8 |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-44 | 3 | |
| β-strand | 47-50 | 4 | 1 |
| β-strand | 61-65 | 5 | 1 |
| β-strand | 77-81 | 5 | 1 |
| α-helix | 82-95 | 14 | |
| α-helix | 97-99 | 3 | |
| α-helix | 102-116 | 15 | |
| α-helix | 121-124 | 4 | |
Chain C: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-50 | 3 | |
| α-helix | 52-54 | 3 | |
| α-helix | 56-61 | 6 | |
| α-helix | 67-70 | 4 | |
| β-strand | 75 | 1 | 4 |
| β-strand | 109-111 | 3 | 9 |
| β-strand | 114-123 | 10 | 9 |
| α-helix | 125-133 | 9 | |
| β-strand | 140-141 | 2 | 9 |
| α-helix | 143-145 | 3 | |
| α-helix | 149-153 | 5 | |
| β-strand | 162-163 | 2 | 9 |
| β-strand | 167 | 1 | 10 |
| β-strand | 175 | 1 | 10 |
| β-strand | 185 | 1 | 9 |
| β-strand | 193-195 | 3 | 9 |
| β-strand | 203-204 | 2 | 9 |
| β-strand | 212-218 | 7 | 9 |
Chain H: 7 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 10-12 | 3 | 12 |
| β-strand | 18-25 | 8 | 11 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 12 |
| β-strand | 46-51 | 6 | 12 |
| β-strand | 57-59 | 3 | 12 |
| β-strand | 67-72 | 6 | 11 |
| β-strand | 77-82 | 6 | 11 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 12 |
| β-strand | 98-99 | 2 | 13 |
| β-strand | 102-103 | 2 | 13 |
| β-strand | 109 | 1 | 12 |
| β-strand | 113-117 | 5 | 12 |
| β-strand | 123 | 1 | 14 |
| α-helix | 124-125 | 2 | |
| β-strand | 126-130 | 5 | 15 |
| β-strand | 142-151 | 10 | 15 |
| β-strand | 152 | 1 | 14 |
| β-strand | 157-160 | 4 | 16 |
| α-helix | 161-163 | 3 | |
| β-strand | 165 | 1 | 16 |
| β-strand | 169-176 | 8 | 15 |
| α-helix | 177 | 1 | |
| β-strand | 182-190 | 9 | 15 |
| α-helix | 192-196 | 5 | |
| β-strand | 201-206 | 6 | 16 |
| α-helix | 207-209 | 3 | |
| β-strand | 211-216 | 6 | 16 |
Chain L: 9 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 17 |
| β-strand | 9-12 | 4 | 18 |
| β-strand | 18-23 | 6 | 17 |
| α-helix | 27-29 | 3 | |
| β-strand | 33-37 | 5 | 18 |
| β-strand | 44-47 | 4 | 18 |
| β-strand | 48 | 1 | 19 |
| β-strand | 52 | 1 | 19 |
| β-strand | 61-66 | 6 | 17 |
| β-strand | 69-74 | 6 | 17 |
| α-helix | 79-81 | 3 | |
| β-strand | 83-91 | 9 | 18 |
| α-helix | 93-95 | 3 | |
| β-strand | 98-101 | 4 | 18 |
| β-strand | 105-109 | 5 | 18 |
| α-helix | 113-114 | 2 | |
| β-strand | 115 | 1 | 20 |
| α-helix | 116-117 | 2 | |
| β-strand | 118-122 | 5 | 21 |
| α-helix | 123-125 | 3 | |
| α-helix | 126-130 | 5 | |
| β-strand | 136-143 | 8 | 21 |
| β-strand | 144 | 1 | 20 |
| β-strand | 149-154 | 6 | 22 |
| β-strand | 157-159 | 3 | 22 |
| β-strand | 163-165 | 3 | 21 |
| α-helix | 166-168 | 3 | |
| β-strand | 169-170 | 2 | 21 |
| β-strand | 176-182 | 7 | 21 |
| α-helix | 186-191 | 6 | |
| β-strand | 195-201 | 7 | 22 |
| β-strand | 204-210 | 7 | 22 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein H | A | protein | 697 | Human herpesvirus 4 | P03231 (AlphaFold model) |
| Envelope glycoprotein L | B | protein | 139 | Human herpesvirus 4 | Q1HVF6 |
| Glycoprotein 42 | C | protein | 227 | Human herpesvirus 4 | P03205 (AlphaFold model) |
| Antibody Fab AMMO1 heavy chain | H | protein | 226 | Homo sapiens | P01857 (AlphaFold model) |
| Antibody Fab AMMO1 light chain | L | protein | 216 | Homo sapiens | Q8N355 |
Sequence of entity 1 (A), FASTA
>6C5V_1 Envelope glycoprotein H (chains A)
MDAMKRGLCCVLLLCGAVFVSPSASSLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPE
ALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVIS
GLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAM
TSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFV
HYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFE
VSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAA
MLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPL
HTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESG
LFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSYAVDGFLGRLSLEREDRDAWHLPAYK
CVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVA
GEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDN
LHVHYLLLTTNGTVMEIAGLYEERAHGSGSGHHHHHH
Sequence of entity 2 (B), FASTA
>6C5V_2 Envelope glycoprotein L (chains B)
MDAMKRGLCCVLLLCGAVFVSPSASWAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDG
FSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSF
SVEDLFGANLNRYAWHRGG
Sequence of entity 3 (C), FASTA
>6C5V_3 Glycoprotein 42 (chains C)
MDAMKRGLCCVLLLCGAVFVSPSASGGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTA
EQEYGDKEVKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNG
CFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQI
FGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNSGSGSGHHHHHH
Sequence of entity 4 (H), FASTA
>6C5V_4 Antibody Fab AMMO1 heavy chain (chains H)
QVQLVQSGADVKKPGASVKVSCKASGYTFIHFGISWVRQAPGQGLEWMGWIDTNNGNTNY
AQSLQGRVTMTTDTSTGTAYMELRSLSTDDTAVYFCARALEMGHRSGFPFDYWGQGVLVT
VSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC
Sequence of entity 5 (L), FASTA
>6C5V_5 Antibody Fab AMMO1 light chain (chains L)
SYELTQPPSVSVAPGQRATITCGGHNIGAKNVHWYQQKPGQAPVLVIQYDSDRPSGIPER
FSGSNSGSTATLTISRVEAGDEADYYCQVWDSGRGHPLYVFGGGTKVTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 8 |
Primary citation
An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus. Snijder, J., Ortego, M.S., Weidle, C. et al. Immunity (2018) 48:799-811.e9. DOI 10.1016/j.immuni.2018.03.026 · PubMed
Other PDB entries of the same protein (UniProt P03231 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7CZE 3.0 Å, Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand…
- 7S1B 3.03 Å, Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with…
- 5T1D 3.1 Å, Crystal structure of EBV gHgL/gp42/E1D1 complex
- 5W0K 3.1 Å, Crystal structure of EBV gHgL/CL40/gp42 N-domain
- 8TNT 3.15 Å, Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and…
- 7S07 3.29 Å, Crystal structure of Epstein-Barr virus glycoprotein gH/gL/gp42-peptide in complex with…
- 8TNN 3.36 Å, Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10
- 7YP2 3.52 Å, Cryo-EM structure of EBV gHgL-gp42 in complex with mAb 6H2 (localized refinement)
- 7YP1 3.54 Å, Cryo-EM structure of EBV gHgL-gp42 in complex with mAb 10E4 (localized refinement)
- 3PHF 3.58 Å, Crystal Structure of the Epstein-Barr virus gH and gL complex
Browse structure collections
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