7M30: Envelope glycoprotein L
Cryo-EM structure of the HCMV pentamer bound by antibodies 1-103, 1-32 and 2-25. Determined by electron microscopy at 3.81 Å resolution. Released 11 Aug 2021.
- Method
- Electron microscopy
- Resolution
- 3.81 Å
- Organisms
- Human cytomegalovirus, Homo sapiens
- Chains
- 10
- Atoms
- 9,191
- Mol. weight
- 224.41 kDa
- Ligands
- NAG
- Released
- 11 Aug 2021
Explore 7M30 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7M30 contains 33 α-helices and 86 β-strands across 10 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 B: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 103-112 | 10 | |
| α-helix | 118-125 | 8 | |
| α-helix | 133-141 | 9 | |
| β-strand | 151-154 | 4 | 1 |
| β-strand | 159-162 | 4 | 1 |
Chain C: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 45-50 | 6 | 2 |
| β-strand | 53-58 | 6 | 2 |
| β-strand | 61-65 | 5 | 2 |
| α-helix | 72-77 | 6 | |
| α-helix | 78-83 | 6 | |
| α-helix | 86-90 | 5 | |
| α-helix | 94-96 | 3 | |
| β-strand | 101-103 | 3 | 3 |
| β-strand | 109-111 | 3 | 3 |
| α-helix | 118-120 | 3 | |
| β-strand | 121-122 | 2 | 3 |
| β-strand | 125 | 1 | 4 |
| β-strand | 130-132 | 3 | 5 |
| α-helix | 146-155 | 10 | |
Chain D: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-56 | 8 | |
| α-helix | 68-70 | 3 | |
| β-strand | 71-78 | 8 | 1 |
| α-helix | 81-83 | 3 | |
| β-strand | 87-93 | 7 | 1 |
| β-strand | 98-102 | 5 | 1 |
| α-helix | 105-117 | 13 | |
| α-helix | 121-130 | 10 | |
| α-helix | 141-150 | 10 | |
| β-strand | 155-165 | 11 | 5 |
| β-strand | 168-182 | 15 | 5 |
| β-strand | 188-198 | 11 | 5 |
| β-strand | 212 | 1 | 4 |
Chain E: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-26 | 5 | |
| α-helix | 36-40 | 5 | |
| α-helix | 42-45 | 4 | |
| α-helix | 46-68 | 23 | |
| α-helix | 74-78 | 5 | |
| α-helix | 82-94 | 13 | |
| β-strand | 98 | 1 | 5 |
| β-strand | 107-114 | 8 | 5 |
| β-strand | 117-126 | 10 | 5 |
Chain F: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 6 |
| β-strand | 10-12 | 3 | 7 |
| β-strand | 18-25 | 8 | 6 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 7 |
| β-strand | 46-52 | 7 | 7 |
| β-strand | 57-59 | 3 | 7 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72 | 6 | 6 |
| β-strand | 77-82 | 6 | 6 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 7 |
| β-strand | 100E-103 | 4 | 7 |
| β-strand | 107-111 | 5 | 7 |
Chain G: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 8 |
| β-strand | 9-12 | 3 | 9 |
| β-strand | 19-24 | 6 | 8 |
| α-helix | 28-30 | 3 | |
| β-strand | 34-38 | 5 | 9 |
| β-strand | 44-48 | 5 | 9 |
| β-strand | 49 | 1 | 10 |
| β-strand | 53 | 1 | 10 |
| β-strand | 62-67 | 6 | 8 |
| β-strand | 70-75 | 6 | 8 |
| α-helix | 80-82 | 3 | |
| β-strand | 84-92 | 9 | 9 |
| β-strand | 95-98 | 4 | 9 |
| β-strand | 102-105 | 4 | 9 |
Chain H: 2 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 11 |
| 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 | 103 | 1 | 12 |
| β-strand | 107-109 | 3 | 12 |
Chain L: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 13 |
| β-strand | 10-12 | 3 | 14 |
| α-helix | 17-18 | 2 | |
| β-strand | 19-25 | 7 | 13 |
| β-strand | 33-38 | 6 | 14 |
| β-strand | 45-49 | 5 | 14 |
| β-strand | 53-54 | 2 | 14 |
| α-helix | 55 | 1 | |
| β-strand | 62-66 | 5 | 13 |
| β-strand | 70-75 | 6 | 13 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 14 |
| β-strand | 96-97 | 2 | 14 |
| β-strand | 101-104 | 4 | 14 |
2 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 |
|---|
| Envelope glycoprotein L | B | protein | 248 | Human cytomegalovirus | P16832 |
| Envelope protein UL128 | C | protein | 144 | Human cytomegalovirus | P16837 |
| Envelope glycoprotein UL130 | D | protein | 189 | Human cytomegalovirus | P16772 |
| UL131A | E | protein | 111 | Human cytomegalovirus | F5HET4 (AlphaFold model) |
| 2-25 Fab Heavy Chain | F | protein | 234 | Homo sapiens | |
| 2-25 Fab Light Chain | G | protein | 212 | Homo sapiens | |
| 1-32 Fab Heavy Chain | H | protein | 241 | Homo sapiens | |
| 1-32 Fab Light Chain | L | protein | 213 | Homo sapiens | |
| 1-103 Fab Heavy Chain | M | protein | 232 | Homo sapiens | |
| 1-103 Fab Light Chain | N | protein | 210 | Homo sapiens | |
Sequence of entity 1 (B), FASTA
>7M30_1 Envelope glycoprotein L (chains B)
VAVSVAPTAAEKVPAECPELTRRCLLGEVFQGDKYESWLRPLVNVTRRDGPLSQLIRYRP
VTPEAANSVLLDDAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPA
VYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPV
STAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRY
GPQAVDAR
Sequence of entity 2 (C), FASTA
>7M30_2 Envelope protein UL128 (chains C)
EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQ
VVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLD
QYLESVKKHKRLDVCRAKMGYMLQ
Sequence of entity 3 (D), FASTA
>7M30_3 Envelope glycoprotein UL130 (chains D)
SPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRN
ETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAK
IFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYT
FCTHPNLIV
Sequence of entity 4 (E), FASTA
>7M30_4 UL131A (chains E)
QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLK
RINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN
Sequence of entity 5 (F), FASTA
>7M30_5 2-25 Fab Heavy Chain (chains F)
QVQLVESGAEVKKPGASVKVSCKASGYTFTNYAIHWVRQAPGQRLEWMGWINAGRGNTKY
SQKFQGRVTITRDTSASTAYMELSSLRSEDAAVYFCARDESTGDYYYYMDVWGKGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ
Sequence of entity 6 (G), FASTA
>7M30_6 2-25 Fab Light Chain (chains G)
SYELTQPPSVSVSPGQTASITCSGDRLDDKYASWYQQKAGQSPVLVIYQDNKRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCQAWDSDTYVFGTGTKVTVLGQPKAAPSVTLFPP
SSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSL
TPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS
Sequence of entity 7 (H), FASTA
>7M30_7 1-32 Fab Heavy Chain (chains H)
QVKLVESGGGVVQPGRSLRLSCAGSGFAFDNYAMHWVRQAPGKGLEWVAVISLEGRNKYY
AGPAKGRFSISRDNSRNTVHLQMNSLRPEDTAVYFCARDMRYYYDSNGHYRNRYGMDVWG
QGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLF
Q
Sequence of entity 8 (L), FASTA
>7M30_8 1-32 Fab Light Chain (chains L)
DIQMTQSPSSLSASVGDSVTITCQASQDINQFVSWYQQKPGKPPKLLIYDASNLESGVPS
RFSGSGSGTHFTFTISSLQPDDIATYYCQQYENLFTFGPGTKVDIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 9 (M), FASTA
>7M30_9 1-103 Fab Heavy Chain (chains M)
QLQLQESGPGLVKPSETLSLTCSVSGDAISGSNYYWGWIRQPPGKGLQWIGSIYHTGSTF
YNPSFSSRVTLSVDTSKNQFSLKLISVNAADTAVYYCARRIRGYSGTYDWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ
Sequence of entity 10 (N), FASTA
>7M30_10 1-103 Fab Light Chain (chains N)
DIQLTQSPSFLSASVGDRVTITCRASQDISSYVAWYQQKPGNAPKLLISSASTLPSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQLNNFGPGTTVDIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Primary citation
Structural basis for HCMV Pentamer recognition by neuropilin 2 and neutralizing antibodies. Wrapp, D., Ye, X., Ku, Z. et al. Sci Adv (2022) 8:eabm2546-eabm2546. DOI 10.1126/sciadv.abm2546 · PubMed
Other PDB entries of the same protein (UniProt P16832), best resolution first:
- 8TCO 2.8 Å, HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
- 7RAM 3.43 Å, Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex…
Browse structure collections
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