7T4Q: HCMV Pentamer gH/gL/UL128/UL130/UL131A
CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11. Determined by electron microscopy at 2.9 Å resolution. Released 23 Mar 2022.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Human betaherpesvirus 5, Homo sapiens
- Chains
- 11
- Atoms
- 15,473
- Mol. weight
- 340.98 kDa
- Ligands
- NAG
- Released
- 23 Mar 2022
Explore 7T4Q in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7T4Q contains 97 α-helices and 136 β-strands across 11 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: 37 helices, 40 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-48 | 2 | |
| β-strand | 49-52 | 4 | 1 |
| β-strand | 57 | 1 | 2 |
| β-strand | 66 | 1 | 3 |
| β-strand | 69-72 | 4 | 1 |
| β-strand | 76-79 | 4 | 4 |
| β-strand | 83 | 1 | 5 |
| β-strand | 86 | 1 | 5 |
| β-strand | 87 | 1 | 3 |
| β-strand | 89-92 | 4 | 4 |
| α-helix | 95-97 | 3 | |
| α-helix | 100-106 | 7 | |
| α-helix | 115-122 | 8 | |
| β-strand | 125-126 | 2 | 6 |
| α-helix | 133-135 | 3 | |
| β-strand | 136-137 | 2 | 7 |
| α-helix | 156-158 | 3 | |
| α-helix | 163-164 | 2 | |
| β-strand | 165 | 1 | 8 |
| α-helix | 166 | 1 | |
| α-helix | 188-190 | 3 | |
| β-strand | 194-197 | 4 | 9 |
| β-strand | 204 | 1 | 10 |
| β-strand | 207-210 | 4 | 9 |
| β-strand | 212-217 | 6 | 7 |
| β-strand | 219 | 1 | 11 |
| β-strand | 221 | 1 | 11 |
| β-strand | 223-229 | 7 | 7 |
| β-strand | 233-240 | 8 | 7 |
| β-strand | 246-251 | 6 | 7 |
| β-strand | 258 | 1 | 10 |
| α-helix | 259 | 1 | |
| α-helix | 264-267 | 4 | |
| β-strand | 268-271 | 4 | 7 |
| β-strand | 276-280 | 5 | 7 |
| β-strand | 281-282 | 2 | 6 |
| α-helix | 283-286 | 4 | |
| α-helix | 290-293 | 4 | |
| α-helix | 299-302 | 4 | |
| α-helix | 309-312 | 4 | |
| α-helix | 313-318 | 6 | |
| α-helix | 319-327 | 9 | |
| α-helix | 335-352 | 18 | |
| α-helix | 355-358 | 4 | |
| α-helix | 363-384 | 22 | |
| α-helix | 386 | 1 | |
| α-helix | 389 | 1 | |
| α-helix | 392-394 | 3 | |
| α-helix | 397-408 | 12 | |
| β-strand | 415 | 1 | 8 |
| α-helix | 416-428 | 13 | |
| α-helix | 432-434 | 3 | |
| α-helix | 437-453 | 17 | |
| α-helix | 458-460 | 3 | |
| α-helix | 461-474 | 14 | |
| α-helix | 481-494 | 14 | |
| α-helix | 497-505 | 9 | |
| α-helix | 515-518 | 4 | |
| α-helix | 521-523 | 3 | |
| β-strand | 527-528 | 2 | 12 |
| α-helix | 532-536 | 5 | |
| α-helix | 548-558 | 11 | |
| β-strand | 578-581 | 4 | 12 |
| β-strand | 587-592 | 6 | 12 |
| β-strand | 597 | 1 | 13 |
| β-strand | 600-603 | 4 | 12 |
| β-strand | 614-619 | 6 | 12 |
| β-strand | 626 | 1 | 13 |
| β-strand | 637 | 1 | 14 |
| β-strand | 652 | 1 | 15 |
| β-strand | 653-657 | 5 | 14 |
| β-strand | 663-666 | 4 | 14 |
| β-strand | 669 | 1 | 15 |
| α-helix | 672-679 | 8 | |
| α-helix | 681-683 | 3 | |
| β-strand | 694-697 | 4 | 14 |
| β-strand | 703-705 | 3 | 14 |
Chain B: 13 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 59 | 1 | |
| β-strand | 60 | 1 | 2 |
| α-helix | 61-63 | 3 | |
| α-helix | 67-69 | 3 | |
| β-strand | 82-83 | 2 | 16 |
| α-helix | 84-86 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 103-112 | 10 | |
| α-helix | 118-127 | 10 | |
| α-helix | 131-144 | 14 | |
| β-strand | 150-155 | 6 | 17 |
| β-strand | 158-163 | 6 | 17 |
| β-strand | 169-170 | 2 | 16 |
| β-strand | 178-184 | 7 | 4 |
| β-strand | 188-197 | 10 | 4 |
| β-strand | 202-211 | 10 | 4 |
| α-helix | 216-218 | 3 | |
| α-helix | 219-236 | 18 | |
| α-helix | 241-252 | 12 | |
| α-helix | 259-260 | 2 | |
Chain C: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 45-50 | 6 | 18 |
| β-strand | 53-57 | 5 | 18 |
| β-strand | 62-65 | 4 | 18 |
| α-helix | 71-81 | 11 | |
| α-helix | 86-92 | 7 | |
| α-helix | 94-96 | 3 | |
| β-strand | 101-103 | 3 | 19 |
| β-strand | 109-111 | 3 | 19 |
| α-helix | 118-120 | 3 | |
| β-strand | 121-122 | 2 | 19 |
| β-strand | 125 | 1 | 20 |
| β-strand | 130-132 | 3 | 21 |
| α-helix | 137-140 | 4 | |
| α-helix | 146-155 | 10 | |
Chain D: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 54-56 | 3 | |
| α-helix | 62-65 | 4 | |
| α-helix | 68-70 | 3 | |
| β-strand | 71-77 | 7 | 17 |
| α-helix | 81-83 | 3 | |
| β-strand | 88-93 | 6 | 17 |
| β-strand | 98-102 | 5 | 17 |
| α-helix | 105-117 | 13 | |
| α-helix | 120-129 | 10 | |
| α-helix | 141-150 | 10 | |
| β-strand | 154-165 | 12 | 21 |
| β-strand | 168-182 | 15 | 21 |
| β-strand | 188-198 | 11 | 21 |
| β-strand | 212 | 1 | 20 |
Chain E: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-25 | 4 | |
| α-helix | 36-40 | 5 | |
| α-helix | 42-45 | 4 | |
| α-helix | 46-68 | 23 | |
| α-helix | 77-79 | 3 | |
| α-helix | 82-94 | 13 | |
| β-strand | 97-100 | 4 | 21 |
| β-strand | 105-113 | 9 | 21 |
| β-strand | 117-126 | 10 | 21 |
Chain F: 5 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-29 | 4 | 22 |
| β-strand | 33-35 | 3 | 23 |
| α-helix | 40 | 1 | |
| β-strand | 41-48 | 8 | 22 |
| β-strand | 58-64 | 7 | 23 |
| β-strand | 71-77 | 7 | 23 |
| β-strand | 82-84 | 3 | 23 |
| β-strand | 92-97 | 6 | 22 |
| α-helix | 98-100 | 3 | |
| β-strand | 102-107 | 6 | 22 |
| α-helix | 112-114 | 3 | |
| β-strand | 116-123 | 8 | 23 |
| α-helix | 124 | 1 | |
| β-strand | 125 | 1 | 24 |
| α-helix | 126 | 1 | |
| β-strand | 129 | 1 | 19 |
| β-strand | 131 | 1 | 24 |
| β-strand | 136-137 | 2 | 23 |
| β-strand | 142-146 | 5 | 23 |
Chain G: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26 | 1 | |
| β-strand | 27 | 1 | 25 |
| β-strand | 28 | 1 | 26 |
| β-strand | 32-35 | 4 | 27 |
| β-strand | 41-46 | 6 | 26 |
| β-strand | 58-63 | 6 | 27 |
| β-strand | 70-74 | 5 | 27 |
| β-strand | 78 | 1 | 27 |
| α-helix | 79-80 | 2 | |
| β-strand | 87-92 | 6 | 26 |
| β-strand | 95-100 | 6 | 26 |
| α-helix | 105-107 | 3 | |
| β-strand | 110-118 | 9 | 27 |
| β-strand | 122-126 | 5 | 27 |
| β-strand | 127 | 1 | 25 |
| α-helix | 128-129 | 2 | |
| β-strand | 130-134 | 5 | 27 |
Chain H: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-30 | 4 | 28 |
| β-strand | 33-36 | 4 | 29 |
| α-helix | 41 | 1 | |
| β-strand | 42-48 | 7 | 28 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-62 | 6 | 29 |
| β-strand | 69-73 | 5 | 29 |
| β-strand | 77-78 | 2 | 29 |
| α-helix | 79 | 1 | |
| β-strand | 86-91 | 6 | 28 |
| β-strand | 94-99 | 6 | 28 |
| α-helix | 104-106 | 3 | |
| β-strand | 109-114 | 6 | 29 |
| β-strand | 121 | 1 | 29 |
| β-strand | 125-129 | 5 | 29 |
3 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 H | A | protein | 767 | Human betaherpesvirus 5 | Q6SW67 (AlphaFold model) |
| Envelope glycoprotein L | B | protein | 278 | Human betaherpesvirus 5 | F5HCH8 (AlphaFold model) |
| Envelope protein UL128 | C | protein | 171 | Human betaherpesvirus 5 | V9LLX6 |
| Envelope glycoprotein UL130 | D | protein | 254 | Human betaherpesvirus 5 | F5HCP3 (AlphaFold model) |
| Envelope protein UL131A | E | protein | 129 | Human betaherpesvirus 5 | F5HET4 |
| Fab 2C12 heavy chain | F | protein | 252 | Homo sapiens | |
| Fab 2C12 light chain | G | protein | 240 | Homo sapiens | |
| Fab 7I13 light chain | H | protein | 237 | Homo sapiens | |
| Fab 7I13 heavy chain | I | protein | 251 | Homo sapiens | |
| Fab 13H11 heavy chain | J | protein | 250 | Homo sapiens | |
| Fab 13H11 light chain | K | protein | 237 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>7T4Q_1 Envelope glycoprotein H (chains A)
MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCT
YNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQ
RLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTES
HTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSI
DDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDA
ALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQ
VSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLV
RLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVH
TTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFP
DATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGI
SYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDT
QGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGTKLG
PEQKLISEEDLNSAVDGSGLNDIFEAQKIEWHENLYFQGHHHHHHHH
Sequence of entity 2 (B), FASTA
>7T4Q_2 Envelope glycoprotein L (chains B)
MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVF
EGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLR
ALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLG
FELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDP
PLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR
Sequence of entity 3 (C), FASTA
>7T4Q_3 Envelope protein UL128 (chains C)
MSPKNLTPFLTALWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPD
GEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQY
LLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ
Sequence of entity 4 (D), FASTA
>7T4Q_4 Envelope glycoprotein UL130 (chains D)
MLRLLLRHHFHCLLLCAVWATPCLASPWFTLTANQNPSPPWSKLTYPKPHDAATFYCPFL
YPSPPRSPSQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQT
ILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWA
HVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQGSAWSHPQFEKGGGSGGG
SGGGSAWSHPQFEK
Sequence of entity 5 (E), FASTA
>7T4Q_5 Envelope protein UL131A (chains E)
MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLT
LNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSL
EFSVRLFAN
Sequence of entity 6 (F), FASTA
>7T4Q_6 Fab 2C12 heavy chain (chains F)
MKKNIAFLLASMFVFSIATNAYAQITLRESGPTLVKPTQTLTLTCTFSGFSLNTNGVGVG
WIRQPPGKALEWLALIYWNGNEGYSPSLKSRLTITKDTSKNQVVLTMTNMDPVDTATYYC
VHWPQGLTTVTRLAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDY
FPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNT
KVDKKVEPKSCD
Sequence of entity 7 (G), FASTA
>7T4Q_7 Fab 2C12 light chain (chains G)
MKKNIAFLLASMFVFSIATNAYAQSALTQPRSVSGSPGQSVTISCTGTTSDVGRYNFVSW
YQQHPGKAPKLLMYDVSQRPSGVPSRFSGSKSGNTASLTISGLQAEDEAVFYCCSYAGGN
FFSYVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKAD
SSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC
Sequence of entity 8 (H), FASTA
>7T4Q_8 Fab 7I13 light chain (chains H)
MKKNIAFLLASMFVFSIATNAYAEIVLTQSPGTLSLSPGERATLSCRASQSVSSDFLAWY
QQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYAASPP
FGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 9 (I), FASTA
>7T4Q_9 Fab 7I13 heavy chain (chains I)
MKKNIAFLLASMFVFSIATNAYAQVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGMHWV
RQGPGKGLEWVAVISYDASSKYYTDSVQGRFTISRDNSKNTLFLQMNSLRGEDTAVYYCA
KALRYLDWFLSDPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYF
PEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK
VDKKVEPKSCD
Sequence of entity 10 (J), FASTA
>7T4Q_10 Fab 13H11 heavy chain (chains J)
MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWV
RQAPGQGLEWMGIIHPSSGGTSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCG
RAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCD
Sequence of entity 11 (K), FASTA
>7T4Q_11 Fab 13H11 light chain (chains K)
MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQ
QKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFT
FGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 6 |
Primary citation
Structural basis for HCMV Pentamer receptor recognition and antibody neutralization. Kschonsak, M., Johnson, M.C., Schelling, R. et al. Sci Adv (2022) 8:eabm2536-eabm2536. DOI 10.1126/sciadv.abm2536 · PubMed
Other PDB entries of the same protein (UniProt Q6SW67 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7LBG 2.6 Å, CryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth…
- 7LBF 2.8 Å, CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth…
- 7LBE 2.9 Å, CryoEM structure of the HCMV Trimer gHgLgO in complex with neutralizing fabs 13H11 and…
- 5VOB 3.02 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
- 7T4S 3.1 Å, CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and…
- 7T4R 3.3 Å, CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and…
- 5VOC 3.99 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low…
- 5VOD 5.9 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6
Browse structure collections
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