5VOD: HCMV Pentamer
Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6. Determined by X-ray diffraction at 5.9 Å resolution. Released 5 Jul 2017.
- Method
- X-ray diffraction
- Resolution
- 5.9 Å
- Organisms
- Human cytomegalovirus, Human cytomegalovirus (strain 5508), Human cytomegalovirus (strain AD169)
- Chains
- 7
- Atoms
- 14,001
- Mol. weight
- 237.95 kDa
- Released
- 5 Jul 2017
Explore 5VOD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5VOD contains 70 α-helices and 108 β-strands across 7 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: 40 helices, 35 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 49-51 | 3 | 1 |
| β-strand | 57 | 1 | 2 |
| β-strand | 65-66 | 2 | 3 |
| β-strand | 69-71 | 3 | 1 |
| β-strand | 76-83 | 8 | 3 |
| β-strand | 86-92 | 7 | 3 |
| α-helix | 94-97 | 4 | |
| α-helix | 100-106 | 7 | |
| α-helix | 115-122 | 8 | |
| β-strand | 125 | 1 | 4 |
| α-helix | 126-127 | 2 | |
| α-helix | 134-135 | 2 | |
| β-strand | 136-137 | 2 | 5 |
| α-helix | 156-158 | 3 | |
| α-helix | 164 | 1 | |
| β-strand | 165 | 1 | 6 |
| α-helix | 166-167 | 2 | |
| β-strand | 182-183 | 2 | 7 |
| α-helix | 189-191 | 3 | |
| β-strand | 193-197 | 5 | 5 |
| β-strand | 204-205 | 2 | 8 |
| β-strand | 207-217 | 11 | 5 |
| β-strand | 224-230 | 7 | 5 |
| β-strand | 233-239 | 7 | 5 |
| β-strand | 246-251 | 6 | 5 |
| β-strand | 257-258 | 2 | 8 |
| α-helix | 259 | 1 | |
| α-helix | 264-267 | 4 | |
| β-strand | 268-271 | 4 | 5 |
| β-strand | 276-280 | 5 | 5 |
| β-strand | 282 | 1 | 4 |
| α-helix | 285-287 | 3 | |
| α-helix | 290-292 | 3 | |
| α-helix | 299-302 | 4 | |
| α-helix | 309-315 | 7 | |
| α-helix | 317-327 | 11 | |
| α-helix | 335-352 | 18 | |
| α-helix | 354-358 | 5 | |
| β-strand | 361-362 | 2 | 7 |
| α-helix | 363-384 | 22 | |
| α-helix | 388-390 | 3 | |
| α-helix | 392-394 | 3 | |
| α-helix | 397-408 | 12 | |
| β-strand | 415 | 1 | 6 |
| α-helix | 416-428 | 13 | |
| α-helix | 432-434 | 3 | |
| α-helix | 437-453 | 17 | |
| α-helix | 458-460 | 3 | |
| α-helix | 461-475 | 15 | |
| α-helix | 481-493 | 13 | |
| α-helix | 497-505 | 9 | |
| α-helix | 515-518 | 4 | |
| α-helix | 521-523 | 3 | |
| β-strand | 527-528 | 2 | 9 |
| α-helix | 532-536 | 5 | |
| α-helix | 548-557 | 10 | |
| β-strand | 578-581 | 4 | 9 |
| β-strand | 587-592 | 6 | 9 |
| β-strand | 597 | 1 | 10 |
| β-strand | 600-603 | 4 | 9 |
| β-strand | 614-619 | 6 | 9 |
| α-helix | 623-624 | 2 | |
| β-strand | 626 | 1 | 10 |
| β-strand | 633 | 1 | 9 |
| α-helix | 635-636 | 2 | |
| β-strand | 637-638 | 2 | 11 |
| α-helix | 639 | 1 | |
| α-helix | 645-647 | 3 | |
| β-strand | 652-658 | 7 | 11 |
| β-strand | 663-669 | 7 | 11 |
| α-helix | 672-679 | 8 | |
| α-helix | 682-684 | 3 | |
| β-strand | 692-697 | 6 | 11 |
| β-strand | 703-705 | 3 | 11 |
| α-helix | 707-711 | 5 | |
Chain B: 12 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-56 | 10 | |
| β-strand | 60 | 1 | 2 |
| α-helix | 81 | 1 | |
| β-strand | 82-83 | 2 | 12 |
| α-helix | 84-86 | 3 | |
| α-helix | 103-112 | 10 | |
| α-helix | 118-126 | 9 | |
| α-helix | 133-142 | 10 | |
| β-strand | 150-154 | 5 | 13 |
| β-strand | 158-163 | 6 | 13 |
| β-strand | 169-170 | 2 | 12 |
| α-helix | 173-175 | 3 | |
| β-strand | 178-184 | 7 | 3 |
| β-strand | 188-197 | 10 | 3 |
| α-helix | 199-201 | 3 | |
| β-strand | 202-211 | 10 | 3 |
| α-helix | 216-218 | 3 | |
| α-helix | 219-235 | 17 | |
| α-helix | 241-252 | 12 | |
| α-helix | 259-261 | 3 | |
Chain C: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 45-48 | 4 | 14 |
| β-strand | 54-57 | 4 | 14 |
| β-strand | 62-65 | 4 | 14 |
| α-helix | 70-80 | 11 | |
| α-helix | 81-83 | 3 | |
| α-helix | 86-92 | 7 | |
| β-strand | 101-102 | 2 | 15 |
| β-strand | 103 | 1 | 16 |
| β-strand | 109 | 1 | 16 |
| β-strand | 121-122 | 2 | 15 |
| β-strand | 125 | 1 | 17 |
| β-strand | 132 | 1 | 18 |
| α-helix | 146-154 | 9 | |
Chain D: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-56 | 4 | |
| α-helix | 62-65 | 4 | |
| α-helix | 68-70 | 3 | |
| β-strand | 71-78 | 8 | 13 |
| α-helix | 81-83 | 3 | |
| β-strand | 87-93 | 7 | 13 |
| β-strand | 98-102 | 5 | 13 |
| α-helix | 105-117 | 13 | |
| 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 |
| β-strand | 212 | 1 | 17 |
Chain E: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 97-98 | 2 | 18 |
| β-strand | 107-109 | 3 | 18 |
| β-strand | 111-113 | 3 | 18 |
| β-strand | 117-126 | 10 | 18 |
Chain H: 2 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-25 | 4 | 19 |
| β-strand | 30 | 1 | 20 |
| β-strand | 41-44 | 4 | 19 |
| β-strand | 53-58 | 6 | 21 |
| β-strand | 64-70 | 7 | 21 |
| β-strand | 77-78 | 2 | 21 |
| β-strand | 88-92 | 5 | 19 |
| β-strand | 97-101 | 5 | 19 |
| β-strand | 112-117 | 6 | 21 |
| β-strand | 130 | 1 | 21 |
| β-strand | 137 | 1 | 20 |
| β-strand | 149-151 | 3 | 22 |
| β-strand | 166-172 | 7 | 22 |
| β-strand | 178 | 1 | 23 |
| β-strand | 181 | 1 | 24 |
| β-strand | 186 | 1 | 24 |
| β-strand | 191-192 | 2 | 22 |
| α-helix | 193-195 | 3 | |
| β-strand | 197 | 1 | 22 |
| β-strand | 203-208 | 6 | 22 |
| β-strand | 225 | 1 | 25 |
| β-strand | 226 | 1 | 23 |
| α-helix | 228-230 | 3 | |
| β-strand | 234 | 1 | 25 |
Chain L: 0 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 26 |
| β-strand | 12-14 | 3 | 27 |
| β-strand | 19-25 | 7 | 26 |
| β-strand | 40-43 | 4 | 28 |
| β-strand | 50-53 | 4 | 28 |
| β-strand | 59 | 1 | 28 |
| β-strand | 68-69 | 2 | 26 |
| β-strand | 75-80 | 6 | 26 |
| β-strand | 89-93 | 5 | 28 |
| β-strand | 110-111 | 2 | 28 |
| β-strand | 112-114 | 3 | 27 |
| β-strand | 124 | 1 | 29 |
| β-strand | 136-141 | 6 | 29 |
| β-strand | 146 | 1 | 30 |
| β-strand | 152-157 | 6 | 31 |
| β-strand | 160-161 | 2 | 31 |
| β-strand | 170-171 | 2 | 32 |
| β-strand | 180 | 1 | 30 |
| β-strand | 181-182 | 2 | 32 |
| β-strand | 184-189 | 6 | 29 |
| β-strand | 198-204 | 7 | 31 |
| β-strand | 212-213 | 2 | 31 |
| β-strand | 216-217 | 2 | 31 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Envelope glycoprotein H | A | protein | 725 | Human cytomegalovirus | Q6SW67 (AlphaFold model) |
| Envelope glycoprotein L | B | protein | 278 | Human cytomegalovirus (strain 5508) | Q68674 |
| Envelope glycoprotein UL128 | C | protein | 171 | Human cytomegalovirus (strain AD169) | P16837 |
| Envelope glycoprotein UL130 | D | protein | 252 | Human cytomegalovirus (strain Merlin) | F5HCP3 (AlphaFold model) |
| Envelope glycoprotein UL131A | E | protein | 129 | Human cytomegalovirus (strain Merlin) | F5HET4 |
| Fab 9I6 heavy chain | H | protein | 288 | Homo sapiens | S6B291 |
| Fab 9I6 light chain | L | protein | 241 | Homo sapiens | Q8TCD0 |
Sequence of entity 1 (A), FASTA
>5VOD_1 Envelope glycoprotein H (chains A)
MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCT
YNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQ
RLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTES
HTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSI
DDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDA
ALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQ
VSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLV
RLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVH
TTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFP
DATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGI
SYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDT
QGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGSGSH
HHHHH
Sequence of entity 2 (B), FASTA
>5VOD_2 Envelope glycoprotein L (chains B)
MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVF
EGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLR
ALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLG
FELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDP
PLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR
Sequence of entity 3 (C), FASTA
>5VOD_3 Envelope glycoprotein UL128 (chains C)
MSPKDLTPFLTTLWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPD
GEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQY
LLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ
Sequence of entity 4 (D), FASTA
>5VOD_4 Envelope glycoprotein UL130 (chains D)
MLRLLLRHHFHCLLLCAVWATPCLASPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFL
YPSPPRSPLQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQT
ILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWA
HVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQAGWSHPQFEKGGGSGGGS
GGGSWSHPQFEK
Sequence of entity 5 (E), FASTA
>5VOD_5 Envelope glycoprotein UL131A (chains E)
MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLT
LNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSL
EFSVRLFAN
Sequence of entity 6 (H), FASTA
>5VOD_6 Fab 9I6 heavy chain (chains H)
MEFGLSWVFLVAILEGVHCEVQLVQSGAEVKKPGESLKISCRESGDTFPAYWIAWVRQMP
GKGLEWMGIIYPIDSETTYSPSFQGQVTISADKSINTAYLQWSSLKASDSAIYYCARGTS
TGLREAFHIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS
WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP
KSCDKSSGLEVLFQGPLGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK
Sequence of entity 7 (L), FASTA
>5VOD_7 Fab 9I6 light chain (chains L)
METPAELLFLLLLWLPDTTGDVVMTQSPLSLAVTLGQPAYISCRSSQSLGYSDGNTYLNW
FQQRPGQSPRRLIYEVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGTYYCMQGTHWP
PMCSFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNA
LQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
C
Primary citation
Structural basis for potent antibody-mediated neutralization of human cytomegalovirus. Chandramouli, S., Malito, E., Nguyen, T. et al. Sci Immunol (2017) 2. DOI 10.1126/sciimmunol.aan1457 · 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
- 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…
Browse structure collections
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