7T4S: HCMV Pentamer gH/gL/UL128/UL130/UL131A
CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11. Determined by electron microscopy at 3.1 Å resolution. Released 23 Mar 2022.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organisms
- Human betaherpesvirus 5, Homo sapiens
- Chains
- 10
- Atoms
- 16,404
- Mol. weight
- 387.93 kDa
- Ligands
- NAG, CA
- Released
- 23 Mar 2022
Explore 7T4S in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7T4S contains 87 α-helices and 132 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 A: 36 helices, 35 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 50-52 | 3 | 1 |
| β-strand | 65-66 | 2 | 2 |
| β-strand | 70-72 | 3 | 1 |
| β-strand | 75-79 | 5 | 3 |
| β-strand | 83 | 1 | 4 |
| β-strand | 86 | 1 | 4 |
| β-strand | 87-88 | 2 | 2 |
| β-strand | 89-93 | 5 | 3 |
| α-helix | 95-98 | 4 | |
| α-helix | 100-106 | 7 | |
| α-helix | 115-122 | 8 | |
| β-strand | 125 | 1 | 5 |
| α-helix | 128-131 | 4 | |
| α-helix | 133-135 | 3 | |
| β-strand | 136-137 | 2 | 6 |
| α-helix | 156-158 | 3 | |
| α-helix | 163-164 | 2 | |
| β-strand | 165 | 1 | 7 |
| α-helix | 166 | 1 | |
| α-helix | 188-190 | 3 | |
| β-strand | 194-197 | 4 | 8 |
| β-strand | 204 | 1 | 9 |
| β-strand | 207-210 | 4 | 8 |
| β-strand | 211-219 | 9 | 6 |
| β-strand | 223-230 | 8 | 6 |
| β-strand | 233-240 | 8 | 6 |
| β-strand | 246-251 | 6 | 6 |
| β-strand | 258 | 1 | 9 |
| α-helix | 259 | 1 | |
| α-helix | 264-266 | 3 | |
| β-strand | 268-271 | 4 | 6 |
| β-strand | 276-280 | 5 | 6 |
| β-strand | 282 | 1 | 5 |
| α-helix | 284-287 | 4 | |
| α-helix | 290-293 | 4 | |
| α-helix | 299-302 | 4 | |
| α-helix | 309-312 | 4 | |
| α-helix | 313-317 | 5 | |
| α-helix | 318-326 | 9 | |
| α-helix | 335-351 | 17 | |
| α-helix | 354-356 | 3 | |
| α-helix | 363-384 | 22 | |
| α-helix | 391-394 | 4 | |
| α-helix | 397-408 | 12 | |
| β-strand | 415 | 1 | 7 |
| 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 | 481-493 | 13 | |
| α-helix | 497-506 | 10 | |
| α-helix | 515-518 | 4 | |
| α-helix | 521-523 | 3 | |
| β-strand | 527-528 | 2 | 10 |
| α-helix | 532-536 | 5 | |
| α-helix | 548-558 | 11 | |
| β-strand | 578-581 | 4 | 10 |
| β-strand | 587-592 | 6 | 10 |
| β-strand | 597 | 1 | 11 |
| β-strand | 600-603 | 4 | 10 |
| β-strand | 614-619 | 6 | 10 |
| α-helix | 623-624 | 2 | |
| β-strand | 626 | 1 | 11 |
| β-strand | 637-638 | 2 | 12 |
| α-helix | 645-647 | 3 | |
| β-strand | 652-658 | 7 | 12 |
| β-strand | 662-669 | 8 | 12 |
| α-helix | 672-678 | 7 | |
| β-strand | 695-697 | 3 | 12 |
| β-strand | 703-705 | 3 | 12 |
Chain B: 12 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 61-63 | 3 | |
| α-helix | 67-69 | 3 | |
| α-helix | 81 | 1 | |
| β-strand | 82-83 | 2 | 13 |
| α-helix | 84-86 | 3 | |
| α-helix | 103-112 | 10 | |
| α-helix | 118-126 | 9 | |
| α-helix | 131-142 | 12 | |
| β-strand | 150-155 | 6 | 14 |
| β-strand | 158-163 | 6 | 14 |
| β-strand | 169-170 | 2 | 13 |
| β-strand | 177-184 | 8 | 3 |
| β-strand | 188-197 | 10 | 3 |
| β-strand | 202-211 | 10 | 3 |
| β-strand | 212 | 1 | 15 |
| β-strand | 215 | 1 | 15 |
| α-helix | 216-218 | 3 | |
| α-helix | 219-235 | 17 | |
| α-helix | 241-252 | 12 | |
| α-helix | 255-257 | 3 | |
Chain C: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 45-47 | 3 | 16 |
| β-strand | 55-57 | 3 | 16 |
| β-strand | 63 | 1 | 16 |
| α-helix | 73-77 | 5 | |
| α-helix | 80-82 | 3 | |
| α-helix | 86-92 | 7 | |
| α-helix | 94-96 | 3 | |
| α-helix | 99-100 | 2 | |
| β-strand | 101-104 | 4 | 17 |
| β-strand | 107-111 | 5 | 17 |
| β-strand | 121-122 | 2 | 17 |
| β-strand | 132-133 | 2 | 18 |
| α-helix | 146-155 | 10 | |
Chain D: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-54 | 6 | |
| α-helix | 62-65 | 4 | |
| α-helix | 68-70 | 3 | |
| β-strand | 71-77 | 7 | 14 |
| α-helix | 81-83 | 3 | |
| β-strand | 88-93 | 6 | 14 |
| β-strand | 98-102 | 5 | 14 |
| α-helix | 105-115 | 11 | |
| α-helix | 120-130 | 11 | |
| α-helix | 141-150 | 10 | |
| β-strand | 154-165 | 12 | 18 |
| β-strand | 168-182 | 15 | 18 |
| β-strand | 188-198 | 11 | 18 |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-27 | 4 | |
| α-helix | 36-39 | 4 | |
| α-helix | 42-45 | 4 | |
| α-helix | 46-68 | 23 | |
| α-helix | 74-78 | 5 | |
| α-helix | 82-94 | 13 | |
| β-strand | 107-114 | 8 | 18 |
| β-strand | 117-126 | 10 | 18 |
Chain F: 8 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 151 | 1 | 19 |
| β-strand | 157-161 | 5 | 20 |
| α-helix | 168-170 | 3 | |
| β-strand | 174-180 | 7 | 19 |
| β-strand | 185-195 | 11 | 20 |
| β-strand | 212-216 | 5 | 19 |
| β-strand | 225-229 | 5 | 19 |
| α-helix | 234-237 | 4 | |
| β-strand | 238-240 | 3 | 20 |
| β-strand | 244-250 | 7 | 19 |
| β-strand | 259-268 | 10 | 20 |
| β-strand | 279-280 | 2 | 21 |
| α-helix | 290-292 | 3 | |
| β-strand | 293 | 1 | 21 |
| α-helix | 306-308 | 3 | |
| β-strand | 329-344 | 16 | 21 |
| β-strand | 362-366 | 5 | 21 |
| β-strand | 373-374 | 2 | 21 |
| β-strand | 394-410 | 17 | 21 |
| β-strand | 423-428 | 6 | 21 |
| α-helix | 429-431 | 3 | |
| β-strand | 436-437 | 2 | 22 |
| α-helix | 447-449 | 3 | |
| β-strand | 450-452 | 3 | 22 |
| α-helix | 462-465 | 4 | |
| β-strand | 466 | 1 | 22 |
| β-strand | 474 | 1 | 23 |
| α-helix | 481-482 | 2 | |
| β-strand | 488-504 | 17 | 22 |
| β-strand | 506 | 1 | 24 |
| β-strand | 519 | 1 | 24 |
| β-strand | 521-529 | 9 | 22 |
| β-strand | 536 | 1 | 22 |
| β-strand | 549-550 | 2 | 22 |
| β-strand | 559-578 | 20 | 22 |
| β-strand | 585 | 1 | 23 |
| β-strand | 586-592 | 7 | 22 |
Chain H: 1 helix, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 25 |
| β-strand | 10-12 | 3 | 26 |
| β-strand | 18-25 | 8 | 25 |
| β-strand | 34-39 | 6 | 26 |
| β-strand | 45-51 | 7 | 26 |
| β-strand | 58-60 | 3 | 26 |
| β-strand | 69-73 | 5 | 25 |
| β-strand | 78-83 | 6 | 25 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-103 | 12 | 26 |
| β-strand | 106-112 | 7 | 26 |
| β-strand | 116-120 | 5 | 26 |
Chain I: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-5 | 2 | 31 |
| β-strand | 10-12 | 3 | 32 |
| β-strand | 19-25 | 7 | 31 |
| β-strand | 33-38 | 6 | 32 |
| β-strand | 45-49 | 5 | 32 |
| β-strand | 53-54 | 2 | 32 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 31 |
| β-strand | 70-75 | 6 | 31 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 32 |
| β-strand | 98 | 1 | 32 |
| β-strand | 103-106 | 4 | 32 |
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 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 |
| Neuropilin-2 | F | protein | 875 | Homo sapiens | O60462 |
| Fab 8I21 heavy chain | H | protein | 249 | Homo sapiens | |
| Fab 13H11 heavy chain | J | protein | 250 | Homo sapiens | |
| Fab 13H11 light chain | K | protein | 237 | Homo sapiens | |
| Fab 8I21 light chain | I | protein | 238 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>7T4S_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
>7T4S_2 Envelope glycoprotein L (chains B)
MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVF
EGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLR
ALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLG
FELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDP
PLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR
Sequence of entity 3 (C), FASTA
>7T4S_3 Envelope protein UL128 (chains C)
MSPKNLTPFLTALWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPD
GEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQY
LLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ
Sequence of entity 4 (D), FASTA
>7T4S_4 Envelope glycoprotein UL130 (chains D)
MLRLLLRHHFHCLLLCAVWATPCLASPWFTLTANQNPSPPWSKLTYPKPHDAATFYCPFL
YPSPPRSPSQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQT
ILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWA
HVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQGSAWSHPQFEKGGGSGGG
SGGGSAWSHPQFEK
Sequence of entity 5 (E), FASTA
>7T4S_5 Envelope protein UL131A (chains E)
MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLT
LNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSL
EFSVRLFAN
Sequence of entity 6 (F), FASTA
>7T4S_6 Neuropilin-2 (chains F)
MDMFPLTWVFLALYFSRHQVRGQPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVY
APEPNQKIVLNFNPHFEIEKHDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSML
YIKFTSDYARQGAGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTIL
AKPKMEIILQFLIFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRS
STGILSLTFHTDMAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYS
DGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKS
YKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIAL
RLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQ
AQPGEEWLQVDLGTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQD
PRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTDSKPT
VETLGPTVKSEETTTPYPTEEEATECGENCSFEDDKDLQLPSGFNCNFDFLEEPCGWMYD
HAKWLRTTWASSSSPNDRTFPDDRNFLRLQSDSQREGQYARLISPPVHLPRSPVCMEFQY
QATGGRGVALQVVREASQESKLLWVIREDQGGEWKHGRIILPSYDMEYQIVFEGVIGKGR
SGEIAIDDIRISTDVPLENCMEPISAFAGENFKVDIPEIHEREGYEDEIDDEYEVDWSNS
SSATSGSGAPSTDKEKSWLYTLDPGNSDYKDDDDK
Sequence of entity 7 (H), FASTA
>7T4S_7 Fab 8I21 heavy chain (chains H)
MKKNIAFLLASMFVFSIATNAYALVELVESGGGVVQPGRSLRLSCAASGFTFSSDGMHWV
RQSPGRGLEWVAFISSDGSTPYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYFCA
KDWALFRWLRTFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPE
PVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD
KKVEPKSCD
Sequence of entity 8 (J), FASTA
>7T4S_8 Fab 13H11 heavy chain (chains J)
MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWV
RQAPGQGLEWMGIIHPSSGGTSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCG
RAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCD
Sequence of entity 9 (K), FASTA
>7T4S_9 Fab 13H11 light chain (chains K)
MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQ
QKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFT
FGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 10 (I), FASTA
>7T4S_10 Fab 8I21 light chain (chains I)
MKKNIAFLLASMFVFSIATNAYAETVMTQSPATLSVSPGGRATLSCRASQSVGINLAWYQ
QKPGQAPRLLIYGASTRASGFPARFSGSGSGTEFTLTITSLQSEDFAVYYCQQYNDWPPW
TFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQS
GNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 9 |
| CA | Calcium ion | Ca | 1 |
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…
- 7T4Q 2.9 Å, CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with…
- 5VOB 3.02 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
- 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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