7T4R: HCMV Pentamer gH/gL/UL128/UL130/UL131A
CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11. Determined by electron microscopy at 3.3 Å resolution. Released 23 Mar 2022.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organisms
- Homo sapiens, Human betaherpesvirus 5
- Chains
- 19
- Atoms
- 28,717
- Mol. weight
- 638.36 kDa
- Ligands
- NAG
- Released
- 23 Mar 2022
Explore 7T4R in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7T4R contains 164 α-helices and 235 β-strands across 19 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: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-31 | 5 | 1 |
| β-strand | 34-39 | 6 | 1 |
| β-strand | 43 | 1 | 2 |
| α-helix | 45-54 | 10 | |
| β-strand | 58-59 | 2 | 1 |
| α-helix | 60-61 | 2 | |
| α-helix | 65-74 | 10 | |
| β-strand | 85-92 | 8 | 1 |
| β-strand | 109-110 | 2 | 1 |
| β-strand | 122 | 1 | 1 |
| β-strand | 136-141 | 6 | 1 |
| α-helix | 150-151 | 2 | |
| β-strand | 152-156 | 5 | 1 |
| β-strand | 162 | 1 | 2 |
| β-strand | 164-170 | 7 | 1 |
Chain B: 37 helices, 35 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 51-52 | 2 | 3 |
| β-strand | 57 | 1 | 4 |
| β-strand | 66 | 1 | 5 |
| β-strand | 71-72 | 2 | 3 |
| β-strand | 76-80 | 5 | 6 |
| β-strand | 87 | 1 | 5 |
| β-strand | 88-92 | 5 | 6 |
| α-helix | 94-97 | 4 | |
| α-helix | 100-108 | 9 | |
| α-helix | 115-121 | 7 | |
| β-strand | 125 | 1 | 7 |
| α-helix | 126-127 | 2 | |
| α-helix | 128-131 | 4 | |
| α-helix | 133-135 | 3 | |
| β-strand | 137-138 | 2 | 8 |
| α-helix | 156-158 | 3 | |
| β-strand | 165 | 1 | 9 |
| α-helix | 188-190 | 3 | |
| β-strand | 194-197 | 4 | 10 |
| β-strand | 204 | 1 | 11 |
| α-helix | 205-206 | 2 | |
| β-strand | 207-210 | 4 | 10 |
| β-strand | 211-217 | 7 | 8 |
| β-strand | 219 | 1 | 12 |
| β-strand | 221 | 1 | 12 |
| β-strand | 224-230 | 7 | 8 |
| β-strand | 233-239 | 7 | 8 |
| β-strand | 246-251 | 6 | 8 |
| β-strand | 258 | 1 | 11 |
| α-helix | 264-267 | 4 | |
| β-strand | 268-272 | 5 | 8 |
| β-strand | 276-280 | 5 | 8 |
| β-strand | 282 | 1 | 7 |
| α-helix | 283-285 | 3 | |
| α-helix | 290-293 | 4 | |
| α-helix | 299-302 | 4 | |
| α-helix | 309-312 | 4 | |
| α-helix | 313-317 | 5 | |
| α-helix | 318-327 | 10 | |
| α-helix | 335-351 | 17 | |
| α-helix | 355-358 | 4 | |
| α-helix | 363-384 | 22 | |
| α-helix | 391-394 | 4 | |
| α-helix | 397-408 | 12 | |
| β-strand | 415 | 1 | 9 |
| 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 | 1 | 13 |
| α-helix | 532-536 | 5 | |
| α-helix | 548-557 | 10 | |
| α-helix | 573 | 1 | |
| β-strand | 578-581 | 4 | 13 |
| β-strand | 587-592 | 6 | 13 |
| β-strand | 600-603 | 4 | 13 |
| β-strand | 614-619 | 6 | 13 |
| α-helix | 623-624 | 2 | |
| β-strand | 633 | 1 | 13 |
| α-helix | 635-636 | 2 | |
| β-strand | 637-638 | 2 | 14 |
| β-strand | 652-656 | 5 | 14 |
| β-strand | 665-669 | 5 | 14 |
| α-helix | 672-679 | 8 | |
| α-helix | 681-683 | 3 | |
| β-strand | 695-697 | 3 | 14 |
| β-strand | 703-705 | 3 | 14 |
Chain C: 15 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| β-strand | 60 | 1 | 4 |
| α-helix | 61-63 | 3 | |
| α-helix | 67-69 | 3 | |
| β-strand | 83 | 1 | 15 |
| α-helix | 84-86 | 3 | |
| α-helix | 91-93 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 103-112 | 10 | |
| α-helix | 118-126 | 9 | |
| α-helix | 131-142 | 12 | |
| β-strand | 150-155 | 6 | 16 |
| β-strand | 158-163 | 6 | 16 |
| α-helix | 164-166 | 3 | |
| β-strand | 170 | 1 | 15 |
| α-helix | 173-175 | 3 | |
| β-strand | 178-184 | 7 | 6 |
| β-strand | 188-196 | 9 | 6 |
| β-strand | 203-211 | 9 | 6 |
| β-strand | 212 | 1 | 17 |
| β-strand | 215 | 1 | 17 |
| α-helix | 216-218 | 3 | |
| α-helix | 219-235 | 17 | |
| α-helix | 242-251 | 10 | |
| α-helix | 255-257 | 3 | |
Chain D: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-40 | 2 | |
| β-strand | 45 | 1 | 18 |
| β-strand | 50 | 1 | 19 |
| β-strand | 53 | 1 | 19 |
| β-strand | 54-57 | 4 | 18 |
| β-strand | 62-65 | 4 | 18 |
| α-helix | 77-79 | 3 | |
| α-helix | 81-83 | 3 | |
| α-helix | 86-90 | 5 | |
| α-helix | 94-96 | 3 | |
| α-helix | 99-100 | 2 | |
| β-strand | 101-103 | 3 | 20 |
| β-strand | 109-111 | 3 | 20 |
| α-helix | 112-113 | 2 | |
| β-strand | 121-122 | 2 | 20 |
| β-strand | 125 | 1 | 21 |
| β-strand | 130-132 | 3 | 22 |
| α-helix | 146-155 | 10 | |
Chain E: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-56 | 4 | |
| α-helix | 68-70 | 3 | |
| β-strand | 71-77 | 7 | 16 |
| β-strand | 88-93 | 6 | 16 |
| β-strand | 98-101 | 4 | 16 |
| α-helix | 105-116 | 12 | |
| α-helix | 120-129 | 10 | |
| α-helix | 141-150 | 10 | |
| β-strand | 154-165 | 12 | 22 |
| β-strand | 168-182 | 15 | 22 |
| β-strand | 188-198 | 11 | 22 |
| β-strand | 212 | 1 | 21 |
Chain F: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-26 | 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 | 97-99 | 3 | 22 |
| β-strand | 107-113 | 7 | 22 |
| β-strand | 117-126 | 10 | 22 |
Chain G: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 23 |
| β-strand | 10-11 | 2 | 24 |
| β-strand | 18-25 | 8 | 23 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 24 |
| β-strand | 45-51 | 7 | 24 |
| β-strand | 58-60 | 3 | 24 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 23 |
| β-strand | 78-83 | 6 | 23 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 24 |
| β-strand | 110-113 | 4 | 24 |
| β-strand | 117-120 | 4 | 24 |
Chain H: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 25 |
| β-strand | 10 | 1 | 26 |
| β-strand | 19-25 | 7 | 25 |
| β-strand | 33-38 | 6 | 26 |
| β-strand | 45-48 | 4 | 26 |
| β-strand | 54 | 1 | 26 |
| β-strand | 62-67 | 6 | 25 |
| β-strand | 70-75 | 6 | 25 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 26 |
| α-helix | 97 | 1 | |
| β-strand | 98 | 1 | 26 |
| α-helix | 99 | 1 | |
| β-strand | 102-103 | 2 | 26 |
11 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 |
|---|
| Thrombomodulin | A | protein | 527 | Homo sapiens | P07204 (AlphaFold model) |
| Envelope glycoprotein H | B, K | protein | 767 | Human betaherpesvirus 5 | Q6SW67 (AlphaFold model) |
| Envelope glycoprotein L | C, L | protein | 278 | Human betaherpesvirus 5 | F5HCH8 (AlphaFold model) |
| Envelope protein UL128 | D, M | protein | 171 | Human betaherpesvirus 5 | V9LLX6 |
| Envelope glycoprotein UL130 | E, N | protein | 254 | Human betaherpesvirus 5 | F5HCP3 |
| Envelope protein UL131A | F, O | protein | 129 | Human betaherpesvirus 5 | F5HET4 |
| Fab 13H11 heavy chain | G, P | protein | 250 | Homo sapiens | |
| Fab 13H11 light chain | H, Q | protein | 237 | Homo sapiens | |
| Fab MSL-109 light chain | I, R | protein | 257 | Homo sapiens | |
| Fab MSL-109 heavy chain | J, S | protein | 257 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>7T4R_1 Thrombomodulin (chains A)
MLGVLVLGALALAGLGFPAPAEPQPGGSQCVEHDCFALYPGPATFLNASQICDGLRGHLM
TVRSSVAADVISLLLNGDGGVGRRRLWIGLQLPPGCGDPKRLGPLRGFQWVTGDNNTSYS
RWARLDLNGAPLCGPLCVAVSAAEATVPSEPIWEEQQCEVKADGFLCEFHFPATCRPLAV
EPGAAAAAVSITYGTPFAARGADFQALPVGSSAAVAPLGLQLMCTAPPGAVQGHWAREAP
GAWDCSVENGGCEHACNAIPGAPRCQCPAGAALQADGRSCTASATQSCNDLCEHFCVPNP
DQPGSYSCMCETGYRLAADQHRCEDVDDCILEPSPCPQRCVNTQGGFECHCYPNYDLVDG
ECVEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPN
TQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALARHIGTDC
DSGKVDGGDSGSGEPPPSPTPGSTLTPPAVGLVHSGGNSDYKDDDDK
Sequence of entity 2 (B, K), FASTA
>7T4R_2 Envelope glycoprotein H (chains B, K)
MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCT
YNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQ
RLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTES
HTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSI
DDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDA
ALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQ
VSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLV
RLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVH
TTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFP
DATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGI
SYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDT
QGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGTKLG
PEQKLISEEDLNSAVDGSGLNDIFEAQKIEWHENLYFQGHHHHHHHH
Sequence of entity 3 (C, L), FASTA
>7T4R_3 Envelope glycoprotein L (chains C, L)
MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVF
EGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLR
ALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLG
FELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDP
PLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR
Sequence of entity 4 (D, M), FASTA
>7T4R_4 Envelope protein UL128 (chains D, M)
MSPKNLTPFLTALWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPD
GEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQY
LLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ
Sequence of entity 5 (E, N), FASTA
>7T4R_5 Envelope glycoprotein UL130 (chains E, N)
MLRLLLRHHFHCLLLCAVWATPCLASPWFTLTANQNPSPPWSKLTYPKPHDAATFYCPFL
YPSPPRSPSQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQT
ILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWA
HVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQGSAWSHPQFEKGGGSGGG
SGGGSAWSHPQFEK
Sequence of entity 6 (F, O), FASTA
>7T4R_6 Envelope protein UL131A (chains F, O)
MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLT
LNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSL
EFSVRLFAN
Sequence of entity 7 (G, P), FASTA
>7T4R_7 Fab 13H11 heavy chain (chains G, P)
MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWV
RQAPGQGLEWMGIIHPSSGGTSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCG
RAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCD
Sequence of entity 8 (H, Q), FASTA
>7T4R_8 Fab 13H11 light chain (chains H, Q)
MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQ
QKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFT
FGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 9 (I, R), FASTA
>7T4R_9 Fab MSL-109 light chain (chains I, R)
MKKNIAFLLASMFVFSIATNAYADIVMTQSPLSLSVTPGEPASISCRSSQSLLHTNGYNY
LDWYVQKPGQSPQLLIYLASNRASGVPDRFSGSGSGTDFTLKISRVETEDVGVYYCMQAL
QIPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDN
ALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
ECGLNDIFEAQKIEWHE
Sequence of entity 10 (J, S), FASTA
>7T4R_10 Fab MSL-109 heavy chain (chains J, S)
MKKNIAFLLASMFVFSIATNAYAEEQVLESGGGLVKPGGSLRLSCAASGFTFSPYSVFWV
RQAPGKGLEWVSSINSDSTYKYYADSVKGRFTISRDNAENSIFLQMNSLRAEDTAVYYCA
RDRSYYAFSSGSLSDYYYGLDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC
LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNH
KPSNTKVDKKVEPKSCD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 14 |
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 P07204 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1DX5 2.3 Å, Crystal structure of the thrombin-thrombomodulin complex
- 5TO3 2.34 Å, Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a…
- 3GIS 2.4 Å, Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin
- 1HLT 3.0 Å, The structure of a nonadecapeptide of the fifth egf domain of thrombomodulin complexed…
- 1ADX Fifth egf-like domain of thrombomodulin (TMEGF5), NMR, 14 structures
- 1DQB NMR structure of thrombomodulin EGF(4-5)
- 1EGT Thrombin-bound structure of an egf subdomain from human thrombomodulin determined by…
- 1FGD Epidermal growth factor (EGF) subdomain of human thrombomodulin (NMR, 11 structures)
- 1FGE Epidermal growth factor (EGF) subdomain of human thrombomodulin (NMR, 14 structures)
- 1TMR The structure of a 19 residue fragment from the C-loop of the fourth epidermal growth…
- 1ZAQ Fourth egf-like domain of thrombomodulin, NMR, 12 structures
- 2ADX Fifth egf-like domain of thrombomodulin (TMEGF5), NMR, minimized average structure
Browse structure collections
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