8TCO: HCMV Trimer

HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab. Determined by electron microscopy at 2.8 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Human betaherpesvirus 5, Homo sapiens
Chains: 7
Atoms: 13,222
Mol. weight: 269.73 kDa
Ligands: NAG
Released: 9 Aug 2023

Explore 8TCO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TCO contains 78 α-helices and 118 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: 36 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	49-52	4	1
β-strand	57	1	2
β-strand	66	1	3
β-strand	69-72	4	1
β-strand	76-83	8	3
β-strand	86-92	7	3
α-helix	94-97	4
α-helix	100-106	7
α-helix	115-120	6
β-strand	125-126	2	4
α-helix	127	1
α-helix	133-135	3
β-strand	136-137	2	5
α-helix	156-158	3
β-strand	165	1	6
β-strand	183-184	2	7
α-helix	189-191	3
β-strand	193-197	5	8
β-strand	204	1	9
β-strand	207-211	5	8
β-strand	212-217	6	5
β-strand	223-229	7	5
β-strand	233-240	8	5
β-strand	246-251	6	5
β-strand	258	1	9
α-helix	259	1
α-helix	264-267	4
β-strand	268-271	4	5
β-strand	276-280	5	5
β-strand	281-282	2	4
α-helix	283-285	3
α-helix	290-293	4
α-helix	299-302	4
α-helix	309-312	4
α-helix	313-318	6
α-helix	319-325	7
α-helix	335-350	16
α-helix	354-357	4
β-strand	360-361	2	7
α-helix	363-384	22
α-helix	391-394	4
α-helix	397-407	11
β-strand	415	1	6
α-helix	416-418	3
α-helix	423-428	6
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	497-505	9
α-helix	515-518	4
α-helix	532-536	5
α-helix	541-543	3
α-helix	548-558	11
α-helix	573	1
β-strand	578-581	4	10
β-strand	587	1	11
β-strand	589-592	4	10
β-strand	597	1	12
β-strand	601-603	3	10
β-strand	614-616	3	10
β-strand	619	1	11
α-helix	623-624	2
β-strand	626	1	12
β-strand	637-638	2	13
β-strand	652-658	7	13
β-strand	662-669	8	13
α-helix	672-679	8
α-helix	681-683	3
β-strand	693-697	5	13
β-strand	703-705	3	13

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	47-56	10
β-strand	60	1	2
α-helix	67-69	3
β-strand	82	1	14
α-helix	84-86	3
β-strand	96	1	15
α-helix	98	1
β-strand	99-100	2	16
α-helix	103-111	9
α-helix	118-127	10
α-helix	133-136	4
β-strand	139	1	15
β-strand	151-155	5	17
β-strand	158-162	5	17
β-strand	169	1	14
α-helix	173-175	3
β-strand	178-184	7	3
β-strand	188-197	10	3
β-strand	202-211	10	3
β-strand	212	1	18
β-strand	215	1	18
α-helix	216-218	3
α-helix	219-235	17
α-helix	242-252	11
α-helix	255-257	3

Chain C: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	85-87	3	19
β-strand	95-97	3	19
β-strand	106-112	7	19
β-strand	123-130	8	19
β-strand	135-138	4	19
α-helix	142	1
β-strand	144-145	2	19
α-helix	149-161	13
β-strand	173-174	2	20
β-strand	184	1	17
β-strand	186-191	6	15
β-strand	194-199	6	15
α-helix	200-216	17
α-helix	225-230	6
α-helix	231-233	3
β-strand	235-236	2	16
β-strand	240-241	2	21
α-helix	243-252	10
β-strand	255	1	22
α-helix	317	1
β-strand	318	1	22
α-helix	319-320	2
β-strand	321-322	2	20
α-helix	323-336	14
β-strand	341	1	15
α-helix	354-355	2
α-helix	356-361	6
α-helix	362-365	4
β-strand	371	1	23
β-strand	376	1	23
α-helix	380-382	3
β-strand	383-384	2	24
β-strand	413-414	2	24
α-helix	416-423	8
α-helix	425-434	10
α-helix	446-448	3
β-strand	449-450	2	17
α-helix	451-452	2
α-helix	455-458	4

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-12	3	26
β-strand	18-25	8	25
β-strand	33-38	6	26
β-strand	45-48	4	26
β-strand	54	1	26
α-helix	55	1
β-strand	62-65	4	25
β-strand	70-76	7	25
α-helix	80-82	3
β-strand	85-90	6	26
α-helix	95A	1
β-strand	98	1	26
β-strand	102-105	4	26

Chain E: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	27
β-strand	11-12	2	28
β-strand	17-25	9	27
α-helix	29-31	3
β-strand	34-39	6	29
β-strand	45-51	7	29
β-strand	57-59	3	29
β-strand	68	1	27
β-strand	71-72	2	27
β-strand	77-82A	7	27
α-helix	84-86	3
β-strand	88-91	4	29
β-strand	94-95	2	29
β-strand	100H-102	3	29
β-strand	107-109	3	29
β-strand	110-111	2	28

Chain F: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	30
β-strand	10-12	3	31
β-strand	18-25	8	30
β-strand	34-39	6	31
β-strand	45-52	8	31
β-strand	56-59	4	31
α-helix	61-63	3
β-strand	67-72	6	30
β-strand	77-82	6	30
α-helix	84-86	3
β-strand	88-94	7	31
α-helix	98-100A	4
β-strand	100D-100E	2	21
α-helix	100F-100H	3
β-strand	102-103	2	31
β-strand	107-111	5	31

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	10-12	3	33
β-strand	19-25	7	32
β-strand	33-38	6	33
β-strand	45-48	4	33
α-helix	53	1
β-strand	54	1	33
α-helix	55	1
β-strand	62-66	5	32
β-strand	70-75	6	32
α-helix	80-82	3
β-strand	85-90	6	33
β-strand	98	1	33
β-strand	102-105	4	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	743	Human betaherpesvirus 5	P12824
Envelope glycoprotein L	B	protein	268	Human betaherpesvirus 5	P16832
Envelope glycoprotein O	C	protein	466	Human betaherpesvirus 5	P16750
CS4tt1p1_E3K Fab light chain	D	protein	215	Homo sapiens
CS4tt1p1_E3K Fab heavy chain	E	protein	226	Homo sapiens
CS2it1p2_F7K Fab heavy chain	F	protein	229	Homo sapiens
CS2it1p2_F7K Fab light chain	G	protein	234	Homo sapiens

Sequence of entity 1 (A), FASTA

>8TCO_1 Envelope glycoprotein H (chains A)
MRPGLPPYLTVFTVYLLSHLPSQRYGADAASEALDPHAFHLLLNTYGRPIRFLRENTTQC
TYNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQ
QRLNTYALVSKDLASYRSFSQQLKAQDSLGQQPTTVPPPIDLSIPHVWMPPQTTPHDWKG
SHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLMDELRYVKITLTEDFFVVTVS
IDDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKAQLNRHSYLKDSDFLD
AALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGT
EISIPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPDQITDITSL
VRLVYILSKQNQQHLIPQWALRQIADFALQLHKTHLASFLSAFARQELYLMGSLVHSMLV
HTTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLF
PDATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYVVTNQYLIKG
ISYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITAALNISLENCAFCQSALLEYDD
TQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDSRLL
MMSVYALSAIIGIYLLYRMLKTC

Sequence of entity 2 (B), FASTA

>8TCO_2 Envelope glycoprotein L (chains B)
MSVPTQVLGLLLLWLTDARCVAVSVAPTAAEKVPAECPELTRRCLLGEVFQGDKYESWLR
PLVNVTRRDGPLSQLIRYRPVTPEAANSVLLDDAFLDTLALLYNNPDQLRALLTLLSSDT
APRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFN
VVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYY
AGLPPELKQTRVNLPAHSRYGPQAVDAR

Sequence of entity 3 (C), FASTA

>8TCO_3 Envelope glycoprotein O (chains C)
MGRKEMMVRDVPKMVFLISISFLLVSFINCKVMSKALYNRPWRGLVLSKIGKYKLDQLKL
EILRQLETTISTKYNVSKQPVKNLTMNMTEFPQYYILAGPIQNYSITYLWFDFYSTQLRK
PAKYVYSQYNHTAKTITFRPPPCGTVPSMTCLSEMLNVSKRNDTGEQGCGNFTTFNPMFF
NVPRWNTKLYVGPTKVNVDSQTIYFLGLTALLLRYAQRNCTHSFYLVNAMSRNLFRVPKY
INGTKLKNTMRKLKRKQAPVKEQFEKKAKKTQSTTTPYFSYTTSAALNVTTNVTYSITTA
ARRVSTSTIAYRPDSSFMKSIMATQLRDLATWVYTTLRYRQNPFCEPSRNRTAVSEFMKN
THVLIRNETPYTIYGTLDMSSLYYNETMFVENKTASDSNKTTPTSPSMGFQRTFIDPLWD
YLDSLLFLDEIRNFSLRSPTYVNLTPPEHRRAVNLSTLNSLWWWLQ

Sequence of entity 4 (D), FASTA

>8TCO_4 CS4tt1p1_E3K Fab light chain (chains D)
DIQLTQSPSSLSASVGDRVTITCRASQNIYNWLAWYQQKPGQAPKLLIFDASTLEGGVPS
RFGGSGSGTDFTLTISNLRPEDFATYFCQHYYNYPPWTFGQGTKVTFRRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (E), FASTA

>8TCO_5 CS4tt1p1_E3K Fab heavy chain (chains E)
EVRLVESGGGFVQTGGSLRLSCAASGYTFDQYSMHWVRQVPGKGLQFVSTISSNGGSRYY
ADSVKGRFVVSRDEEKEVLYLQMGRLRTDDTGIYFCARAKKIFGGIIPPSGMDVWGRGTT
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 6 (F), FASTA

>8TCO_6 CS2it1p2_F7K Fab heavy chain (chains F)
QVQLVQSGAEVKKPGASVRVSCKVSGYTLTDLSIHWVRQAPGKGLEWMGGFDPEHGEIMY
AQKFQGRVTVTEDTSTHTTYMEVNSLRSEDTAVYYCATDSSIAMTGTYFSDLFALDVWGQ
GTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 7 (G), FASTA

>8TCO_7 CS2it1p2_F7K Fab light chain (chains G)
MRLPAQLLGLLLLWLRGARCDIQMTQSPSSLSASVGDRVTITCRASQTINTNLNWYQQKP
GKAPRLLIFGTFSLKSGVPSRFSGGGSGTDFTLTISSLQPEDFAAYFCQQSHSPPHTFGQ
GTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Single-cell analysis of memory B cells from top neutralizers reveals multiple sites of vulnerability within HCMV Trimer and Pentamer. Zehner, M., Alt, M., Ashurov, A. et al. Immunity (2023) 56:2602-2620.e10. DOI 10.1016/j.immuni.2023.10.009 · PubMed

Other PDB entries of the same protein (UniProt P12824), best resolution first:

7RAM 3.43 Å, Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex…
9DIX 3.51 Å, HCMV gH/UL116/UL141 3-mer complex, ectodomain
9DIY 5.36 Å, Local Cryo-EM structure of HCMV gH/UL116 interaction

Browse structure collections

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