9DIX: HCMV gH/UL116/UL141 3-mer complex, ectodomain
HCMV gH/UL116/UL141 3-mer complex, ectodomain. Determined by electron microscopy at 3.51 Å resolution. Released 20 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 3.51 Å
- Organism
- Human betaherpesvirus 5
- Chains
- 6
- Atoms
- 14,728
- Mol. weight
- 291.47 kDa
- Ligands
- NAG
- Released
- 20 Nov 2024
Explore 9DIX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9DIX contains 88 α-helices and 99 β-strands across 6 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: 33 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 77-80 | 4 | 1 |
| β-strand | 90-93 | 4 | 1 |
| α-helix | 95-98 | 4 | |
| α-helix | 101-107 | 7 | |
| α-helix | 116-124 | 9 | |
| β-strand | 126 | 1 | 2 |
| α-helix | 129-132 | 4 | |
| α-helix | 135-136 | 2 | |
| β-strand | 137-138 | 2 | 3 |
| α-helix | 188-190 | 3 | |
| β-strand | 195-198 | 4 | 4 |
| β-strand | 205 | 1 | 5 |
| β-strand | 208-211 | 4 | 4 |
| β-strand | 213-218 | 6 | 3 |
| β-strand | 224-230 | 7 | 3 |
| β-strand | 234-241 | 8 | 3 |
| α-helix | 246 | 1 | |
| β-strand | 247-252 | 6 | 3 |
| α-helix | 253-255 | 3 | |
| β-strand | 259 | 1 | 5 |
| β-strand | 263 | 1 | 6 |
| α-helix | 265-267 | 3 | |
| β-strand | 269-272 | 4 | 3 |
| β-strand | 277-281 | 5 | 3 |
| β-strand | 283 | 1 | 2 |
| α-helix | 284-288 | 5 | |
| α-helix | 291-294 | 4 | |
| α-helix | 300-303 | 4 | |
| α-helix | 310-313 | 4 | |
| α-helix | 314-318 | 5 | |
| α-helix | 319-328 | 10 | |
| α-helix | 336-353 | 18 | |
| α-helix | 364-385 | 22 | |
| α-helix | 401-409 | 9 | |
| α-helix | 417-429 | 13 | |
| α-helix | 433-435 | 3 | |
| α-helix | 438-454 | 17 | |
| α-helix | 459-461 | 3 | |
| α-helix | 462-475 | 14 | |
| α-helix | 482-494 | 13 | |
| α-helix | 498-508 | 11 | |
| α-helix | 517-519 | 3 | |
| α-helix | 522-525 | 4 | |
| β-strand | 528 | 1 | 7 |
| α-helix | 533-538 | 6 | |
| α-helix | 548-558 | 11 | |
| β-strand | 579-582 | 4 | 7 |
| β-strand | 588-593 | 6 | 7 |
| β-strand | 601-604 | 4 | 7 |
| β-strand | 609 | 1 | 8 |
| β-strand | 612 | 1 | 8 |
| β-strand | 615-620 | 6 | 7 |
| α-helix | 635-637 | 3 | |
| β-strand | 638-639 | 2 | 9 |
| α-helix | 646-648 | 3 | |
| β-strand | 653-659 | 7 | 9 |
| β-strand | 665-670 | 6 | 9 |
| α-helix | 673-680 | 8 | |
| α-helix | 682-684 | 3 | |
| β-strand | 693-698 | 6 | 9 |
| β-strand | 704-706 | 3 | 9 |
Chain B: 7 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40 | 1 | 10 |
| β-strand | 43 | 1 | 11 |
| α-helix | 47-50 | 4 | |
| α-helix | 52-54 | 3 | |
| β-strand | 55-56 | 2 | 12 |
| β-strand | 64-65 | 2 | 13 |
| β-strand | 76-83 | 8 | 11 |
| β-strand | 91-96 | 6 | 11 |
| β-strand | 102-105 | 4 | 11 |
| α-helix | 106-109 | 4 | |
| β-strand | 115-119 | 5 | 13 |
| β-strand | 126-130 | 5 | 13 |
| β-strand | 139-146 | 8 | 11 |
| β-strand | 150 | 1 | 10 |
| β-strand | 151-158 | 8 | 11 |
| β-strand | 159-160 | 2 | 12 |
| β-strand | 163-167 | 5 | 14 |
| α-helix | 172-173 | 2 | |
| β-strand | 188 | 1 | 12 |
| α-helix | 192-194 | 3 | |
| β-strand | 195-203 | 9 | 14 |
| β-strand | 206-213 | 8 | 14 |
| α-helix | 224-227 | 4 | |
| α-helix | 235-238 | 4 | |
| β-strand | 248 | 1 | 14 |
Chain C: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 233-235 | 3 | |
| β-strand | 244-249 | 6 | 1 |
| β-strand | 259-265 | 7 | 1 |
| β-strand | 268-272 | 5 | 1 |
| α-helix | 274-288 | 15 | |
| α-helix | 295-301 | 7 | |
| α-helix | 302-304 | 3 | |
| β-strand | 309 | 1 | 6 |
Chain D: 34 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 77-80 | 4 | 15 |
| β-strand | 90-93 | 4 | 15 |
| α-helix | 95-98 | 4 | |
| α-helix | 102-107 | 6 | |
| α-helix | 116-123 | 8 | |
| β-strand | 126 | 1 | 16 |
| α-helix | 129-132 | 4 | |
| α-helix | 135-136 | 2 | |
| β-strand | 137-138 | 2 | 17 |
| α-helix | 188-190 | 3 | |
| β-strand | 195-198 | 4 | 18 |
| β-strand | 205 | 1 | 19 |
| β-strand | 208-211 | 4 | 18 |
| β-strand | 213-218 | 6 | 17 |
| β-strand | 224-230 | 7 | 17 |
| β-strand | 234-241 | 8 | 17 |
| α-helix | 246 | 1 | |
| β-strand | 247-252 | 6 | 17 |
| α-helix | 253-255 | 3 | |
| β-strand | 259 | 1 | 19 |
| β-strand | 263 | 1 | 20 |
| α-helix | 265-267 | 3 | |
| β-strand | 269-272 | 4 | 17 |
| β-strand | 277-281 | 5 | 17 |
| β-strand | 283 | 1 | 16 |
| α-helix | 284-288 | 5 | |
| α-helix | 291-294 | 4 | |
| α-helix | 300-303 | 4 | |
| α-helix | 310-313 | 4 | |
| α-helix | 314-318 | 5 | |
| α-helix | 319-328 | 10 | |
| α-helix | 336-353 | 18 | |
| α-helix | 364-385 | 22 | |
| α-helix | 401-409 | 9 | |
| α-helix | 417-429 | 13 | |
| α-helix | 433-435 | 3 | |
| α-helix | 438-454 | 17 | |
| α-helix | 459-461 | 3 | |
| α-helix | 462-474 | 13 | |
| α-helix | 475-477 | 3 | |
| α-helix | 482-494 | 13 | |
| α-helix | 498-508 | 11 | |
| α-helix | 517-519 | 3 | |
| α-helix | 522-525 | 4 | |
| β-strand | 528 | 1 | 21 |
| α-helix | 533-538 | 6 | |
| α-helix | 548-558 | 11 | |
| β-strand | 579-582 | 4 | 21 |
| β-strand | 588-593 | 6 | 21 |
| β-strand | 601-609 | 9 | 21 |
| β-strand | 612-620 | 9 | 21 |
| α-helix | 635-637 | 3 | |
| β-strand | 638-639 | 2 | 22 |
| α-helix | 646-648 | 3 | |
| β-strand | 653-659 | 7 | 22 |
| β-strand | 665-670 | 6 | 22 |
| α-helix | 673-680 | 8 | |
| α-helix | 682-684 | 3 | |
| β-strand | 693-698 | 6 | 22 |
| β-strand | 704-706 | 3 | 22 |
Chain E: 7 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40 | 1 | 23 |
| β-strand | 43 | 1 | 24 |
| α-helix | 47-50 | 4 | |
| α-helix | 52-54 | 3 | |
| β-strand | 55-56 | 2 | 25 |
| β-strand | 64-65 | 2 | 26 |
| β-strand | 69-70 | 2 | 26 |
| β-strand | 76-83 | 8 | 24 |
| β-strand | 91-96 | 6 | 24 |
| β-strand | 102-105 | 4 | 24 |
| β-strand | 115-121 | 7 | 26 |
| β-strand | 124-130 | 7 | 26 |
| β-strand | 139-146 | 8 | 24 |
| β-strand | 150 | 1 | 23 |
| β-strand | 151-158 | 8 | 24 |
| β-strand | 159-160 | 2 | 25 |
| β-strand | 162-167 | 6 | 27 |
| α-helix | 172-174 | 3 | |
| β-strand | 188 | 1 | 25 |
| α-helix | 192-194 | 3 | |
| β-strand | 195-203 | 9 | 27 |
| β-strand | 206-213 | 8 | 27 |
| α-helix | 219-221 | 3 | |
| α-helix | 224-227 | 4 | |
| α-helix | 235-238 | 4 | |
| β-strand | 248 | 1 | 27 |
Chain F: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 244-249 | 6 | 15 |
| β-strand | 259-264 | 6 | 15 |
| β-strand | 270-272 | 3 | 15 |
| α-helix | 274-287 | 14 | |
| α-helix | 295-301 | 7 | |
| α-helix | 302-304 | 3 | |
| β-strand | 309 | 1 | 20 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein H | A, D | protein | 680 | Human betaherpesvirus 5 | P12824 |
| Protein UL141 | B, E | protein | 273 | Human betaherpesvirus 5 | Q6RJQ3 (AlphaFold model) |
| UL116 | C, F | protein | 332 | Human betaherpesvirus 5 | Q6SW34 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>9DIX_1 Envelope glycoprotein H (chains A, D)
ASEALDPHAFHLLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYY
VFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSL
GQQPTTVPPPIDLSIPHVWMPPQTTPHDWKGSHTTSGLHRPHFNQTCILFDGHDLLFSTV
TPCLHQGFYLMDELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFI
LRQTEKHELLVLVKKTQLNRHSYLKDSDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSG
RCQMLDRRTVEMAFAYALALFAAARQEEAGTEISIPRALDRQAALLQIQEFMITCLSQTP
PRTTLLLYPTAVDLAKRALWTPDQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFAL
QLHKTHLASFLSAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLA
HPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQPSTLETFPD
LFCLPLGESFSALTVSEHVSYVVTNQYLIKGISYPVSTTVVGQSLIITQTDSQSKCELTR
NMHTTHSITAALNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVS
SPRTHYLMLLKNGTVLEVTD
Sequence of entity 2 (B, E), FASTA
>9DIX_2 Protein UL141 (chains B, E)
SFPFATADIAEKMWAENYETTSPAPVLVAEGEQVTIPCTVMTHSWPMVSIRARFCRSHDG
SDELILDAVKGHRLMNGLQYRLPYATWNFSQLHLGQIFSLTFNVSTDTAGMYECVLRNYS
HGLIMQRFVILTQLETLSRPDEPCCTPALGRYSLGDQIWSPTPWRLRNHDCGMYRGFQRN
YFYIGRADAEDCWKPACPDEEPDRCWTVIQRYRLPGDCYRSQPHPPKFLPVTPAPPADID
TGMSPWATRGGSGGGSLEVLFQGPGHHHHHHHH
Sequence of entity 3 (C, F), FASTA
>9DIX_3 UL116 (chains C, F)
VETNATTVTSTTAAAATTNTTVATTGTTTTSPNVTSTTSNTVITPTTVSSVSNLTSSATS
IPISTSTVSGTRNTRNNNTTTIGTNVTSPSPSVSILTTVTPAATSTTSNNGDVTSDYTPT
FDLENITTTRAPTRPPAQDLCSHNLSIILYEEESQSSVDIAVDEEEPELEDDDEYDELWF
PLYFEAECNLNYTLQYVNHSCDYSVRQSSVSFPPWRDIDSVTFVPRNLSNCSAHGLAVIV
AGNQTWYVNPFSLAHLLDAIYNVLGIEDLSANFRRQLAPYRHTLIVPQTGGSGGSGSDDD
DKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 4 |
Primary citation
A noncanonical glycoprotein H complex enhances cytomegalovirus entry. Norris, M.J., Henderson, L.A., Siddiquey, M.N.A. et al. bioRxiv (2024). DOI 10.1101/2024.10.13.617647 · PubMed
Other PDB entries of the same protein (UniProt P12824), 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…
- 9DIY 5.36 Å, Local Cryo-EM structure of HCMV gH/UL116 interaction
Browse structure collections
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