7M30: Envelope glycoprotein L

Cryo-EM structure of the HCMV pentamer bound by antibodies 1-103, 1-32 and 2-25. Determined by electron microscopy at 3.81 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 3.81 Å
Organisms: Human cytomegalovirus, Homo sapiens
Chains: 10
Atoms: 9,191
Mol. weight: 224.41 kDa
Ligands: NAG
Released: 11 Aug 2021

Explore 7M30 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M30 contains 33 α-helices and 86 β-strands across 10 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 B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	103-112	10
α-helix	118-125	8
α-helix	133-141	9
β-strand	151-154	4	1
β-strand	159-162	4	1

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	45-50	6	2
β-strand	53-58	6	2
β-strand	61-65	5	2
α-helix	72-77	6
α-helix	78-83	6
α-helix	86-90	5
α-helix	94-96	3
β-strand	101-103	3	3
β-strand	109-111	3	3
α-helix	118-120	3
β-strand	121-122	2	3
β-strand	125	1	4
β-strand	130-132	3	5
α-helix	146-155	10

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	49-56	8
α-helix	68-70	3
β-strand	71-78	8	1
α-helix	81-83	3
β-strand	87-93	7	1
β-strand	98-102	5	1
α-helix	105-117	13
α-helix	121-130	10
α-helix	141-150	10
β-strand	155-165	11	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	22-26	5
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	98	1	5
β-strand	107-114	8	5
β-strand	117-126	10	5

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	46-52	7	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
β-strand	100E-103	4	7
β-strand	107-111	5	7

Chain G: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	9-12	3	9
β-strand	19-24	6	8
α-helix	28-30	3
β-strand	34-38	5	9
β-strand	44-48	5	9
β-strand	49	1	10
β-strand	53	1	10
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-92	9	9
β-strand	95-98	4	9
β-strand	102-105	4	9

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	46-51	6	12
β-strand	57-59	3	12
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	103	1	12
β-strand	107-109	3	12

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-12	3	14
α-helix	17-18	2
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-66	5	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	96-97	2	14
β-strand	101-104	4	14

2 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
Envelope glycoprotein L	B	protein	248	Human cytomegalovirus	P16832
Envelope protein UL128	C	protein	144	Human cytomegalovirus	P16837
Envelope glycoprotein UL130	D	protein	189	Human cytomegalovirus	P16772
UL131A	E	protein	111	Human cytomegalovirus	F5HET4 (AlphaFold model)
2-25 Fab Heavy Chain	F	protein	234	Homo sapiens
2-25 Fab Light Chain	G	protein	212	Homo sapiens
1-32 Fab Heavy Chain	H	protein	241	Homo sapiens
1-32 Fab Light Chain	L	protein	213	Homo sapiens
1-103 Fab Heavy Chain	M	protein	232	Homo sapiens
1-103 Fab Light Chain	N	protein	210	Homo sapiens

Sequence of entity 1 (B), FASTA

>7M30_1 Envelope glycoprotein L (chains B)
VAVSVAPTAAEKVPAECPELTRRCLLGEVFQGDKYESWLRPLVNVTRRDGPLSQLIRYRP
VTPEAANSVLLDDAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPA
VYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPV
STAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRY
GPQAVDAR

Sequence of entity 2 (C), FASTA

>7M30_2 Envelope protein UL128 (chains C)
EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQ
VVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLD
QYLESVKKHKRLDVCRAKMGYMLQ

Sequence of entity 3 (D), FASTA

>7M30_3 Envelope glycoprotein UL130 (chains D)
SPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRN
ETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAK
IFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYT
FCTHPNLIV

Sequence of entity 4 (E), FASTA

>7M30_4 UL131A (chains E)
QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLK
RINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

Sequence of entity 5 (F), FASTA

>7M30_5 2-25 Fab Heavy Chain (chains F)
QVQLVESGAEVKKPGASVKVSCKASGYTFTNYAIHWVRQAPGQRLEWMGWINAGRGNTKY
SQKFQGRVTITRDTSASTAYMELSSLRSEDAAVYFCARDESTGDYYYYMDVWGKGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 6 (G), FASTA

>7M30_6 2-25 Fab Light Chain (chains G)
SYELTQPPSVSVSPGQTASITCSGDRLDDKYASWYQQKAGQSPVLVIYQDNKRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCQAWDSDTYVFGTGTKVTVLGQPKAAPSVTLFPP
SSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSL
TPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 7 (H), FASTA

>7M30_7 1-32 Fab Heavy Chain (chains H)
QVKLVESGGGVVQPGRSLRLSCAGSGFAFDNYAMHWVRQAPGKGLEWVAVISLEGRNKYY
AGPAKGRFSISRDNSRNTVHLQMNSLRPEDTAVYFCARDMRYYYDSNGHYRNRYGMDVWG
QGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLF
Q

Sequence of entity 8 (L), FASTA

>7M30_8 1-32 Fab Light Chain (chains L)
DIQMTQSPSSLSASVGDSVTITCQASQDINQFVSWYQQKPGKPPKLLIYDASNLESGVPS
RFSGSGSGTHFTFTISSLQPDDIATYYCQQYENLFTFGPGTKVDIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 9 (M), FASTA

>7M30_9 1-103 Fab Heavy Chain (chains M)
QLQLQESGPGLVKPSETLSLTCSVSGDAISGSNYYWGWIRQPPGKGLQWIGSIYHTGSTF
YNPSFSSRVTLSVDTSKNQFSLKLISVNAADTAVYYCARRIRGYSGTYDWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 10 (N), FASTA

>7M30_10 1-103 Fab Light Chain (chains N)
DIQLTQSPSFLSASVGDRVTITCRASQDISSYVAWYQQKPGNAPKLLISSASTLPSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQLNNFGPGTTVDIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Structural basis for HCMV Pentamer recognition by neuropilin 2 and neutralizing antibodies. Wrapp, D., Ye, X., Ku, Z. et al. Sci Adv (2022) 8:eabm2546-eabm2546. DOI 10.1126/sciadv.abm2546 · PubMed

Other PDB entries of the same protein (UniProt P16832), 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…

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