8TEA: HCMV Pentamer

HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab. Determined by electron microscopy at 3.4 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Human betaherpesvirus 5, Homo sapiens
Chains: 7
Atoms: 6,054
Mol. weight: 153.86 kDa
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8TEA contains 20 α-helices and 69 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 C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	38-39	2
β-strand	45-48	4	1
β-strand	54-58	5	1
β-strand	61-65	5	1
β-strand	69	1	2
α-helix	74-77	4
α-helix	78-83	6
α-helix	86-92	7
α-helix	94-96	3
α-helix	99-100	2
β-strand	101-103	3	3
β-strand	109-111	3	3
β-strand	121-122	2	3
β-strand	125	1	4
β-strand	130-132	3	5

Chain D: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	120-129	10
α-helix	141-150	10
β-strand	154-165	12	5
β-strand	168-182	15	5
β-strand	188-198	11	5
β-strand	212	1	4

Chain E: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	36-39	4
α-helix	42-45	4
α-helix	46-69	24
α-helix	74-79	6
α-helix	82-94	13
β-strand	98-100	3	5
β-strand	105-113	9	5
β-strand	117-126	10	5

Chain F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
β-strand	10-12	3	14
β-strand	18-25	8	13
β-strand	34-39	6	14
β-strand	47-51	5	14
β-strand	58-59	2	14
β-strand	67-70	4	13
β-strand	77-82	6	13
α-helix	84-86	3
β-strand	88-94	7	14
β-strand	102-103	2	14
β-strand	107-111	5	14

Chain G: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	5	1	7
β-strand	9-13	4	8
β-strand	19-24	6	7
β-strand	31	1	2
β-strand	33-38	6	8
β-strand	45-48	4	8
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-92	8	8
β-strand	95B-98	4	8
β-strand	99	1	6
β-strand	102-106	5	8

Chain H: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-11	2	10
β-strand	19-25	7	9
β-strand	32	1	11
β-strand	35-40	6	10
β-strand	44-51	8	10
β-strand	56-57	2	10
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-94	7	10
β-strand	96	1	11
β-strand	97-98	2	12
β-strand	101-102	2	12
β-strand	108-109	2	10
β-strand	113-116	4	10

Chain I: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	5	1	16
β-strand	9-11	2	17
α-helix	13-14	2
β-strand	19-24	6	16
β-strand	33-38	6	17
α-helix	43-44	2
β-strand	45-48	4	17
β-strand	49	1	18
β-strand	53	1	18
β-strand	64-67	4	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-91	8	17
β-strand	96-98	3	17
β-strand	99	1	15
β-strand	102-104	3	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein UL128	C	protein	163	Human betaherpesvirus 5	P16837
Envelope glycoprotein UL130	D	protein	208	Human betaherpesvirus 5	P16772
UL131A	E	protein	130	Human betaherpesvirus 5	Q38M12
CS2pt1p2_A10L Fab light chain	G	protein	216	Homo sapiens
CS2pt1p2_A10L Fab heavy chain	H	protein	243	Homo sapiens
CS3pt1p4_C1L Fab heavy chain	F	protein	223	Homo sapiens
CS3pt1p4_C1L Fab light chain	I	protein	218	Homo sapiens

Sequence of entity 1 (C), FASTA

>8TEA_1 Envelope protein UL128 (chains C)
MEWSWVFLFFLSVTTGVHSEECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPE
KTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSV
PYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ

Sequence of entity 2 (D), FASTA

>8TEA_2 Envelope glycoprotein UL130 (chains D)
MEWSWVFLFFLSVTTGVHSSPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPR
SPLQFSGFQQVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMP
QTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDY
SVSFQVRLTFTEANNQTYTFCTHPNLIV

Sequence of entity 3 (E), FASTA

>8TEA_3 UL131A (chains E)
MEWSWVFLFFLSVTTGVHSQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDL
TLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARS
LEFSVRLFAN

Sequence of entity 4 (G), FASTA

>8TEA_4 CS2pt1p2_A10L Fab light chain (chains G)
QSALTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSNNQRPSGVP
DRFSGSRSGTSASLAISGLRSEDEADYYCAAWDDSLNGRVFGTGTKVTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (H), FASTA

>8TEA_5 CS2pt1p2_A10L Fab heavy chain (chains H)
MEFGLSWVFLVALIKGVQCQVHLEESGGGLVKPGGSLRLSCVASGFSFSDYYMSWIRQAP
GKGLEWLSYISPSGSPTSNADSMKGRFTISRDNARSSLYLQVHSLRVEDTAVYYCARDNT
VFGVVTTPMDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV
EPK

Sequence of entity 6 (F), FASTA

>8TEA_6 CS3pt1p4_C1L Fab heavy chain (chains F)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFTDYALSWVRQAPGQGLEWMGGIIPVLGTPHY
AQKFEDRVTIIADESTGTVFMALSSLRSDDTGMYYCARGVTHPYYYYAMDVWGQGTTITV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 7 (I), FASTA

>8TEA_7 CS3pt1p4_C1L Fab light chain (chains I)
QSALTQPASVSGSPGQSISISCTGTSSDVGAYDYVSWYQQHPGKAPRLIIYDVNKRPSGV
PYRFSGSKSGTAASLTISGLQSEDEAVYYCGSYTSSSAFFYVFGTGTMVTVLRQPKANPT
VTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAA
SSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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 P16837), best resolution first:

5VOB 3.02 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
7M22 3.65 Å, Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2
7M30 3.81 Å, Cryo-EM structure of the HCMV pentamer bound by antibodies 1-103, 1-32 and 2-25
5VOC 3.99 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low…
7KBB 4.02 Å, Cryo-EM structure of the HCMV pentamer bound by Fabs 2-18 and 8I21
5VOD 5.9 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

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