7LBF: HCMV Trimer gHgLgO

CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109. Determined by electron microscopy at 2.8 Å resolution. Released 10 Mar 2021.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Human cytomegalovirus (strain Merlin), Human cytomegalovirus, Homo sapiens
Chains: 8
Atoms: 15,656
Mol. weight: 349.96 kDa
Ligands: NAG
Released: 10 Mar 2021

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

Secondary structure: helices and β-sheets

7LBF contains 87 α-helices and 158 β-strands across 8 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	50-52	3	1
β-strand	57	1	2
β-strand	64-66	3	3
β-strand	70-72	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	115-121	7
β-strand	125	1	4
α-helix	126-127	2
α-helix	133-135	3
β-strand	136-137	2	5
β-strand	145	1	6
α-helix	156-158	3
α-helix	163-164	2
β-strand	165	1	7
α-helix	166	1
β-strand	182-184	3	8
α-helix	188-190	3
β-strand	194-197	4	9
β-strand	204	1	10
β-strand	207-210	4	9
β-strand	212-217	6	5
β-strand	219	1	11
β-strand	221	1	11
β-strand	223-229	7	5
β-strand	233-240	8	5
β-strand	246-251	6	5
β-strand	258	1	10
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	290-293	4
α-helix	299-302	4
β-strand	308	1	6
α-helix	309-312	4
α-helix	313-317	5
α-helix	318-327	10
α-helix	335-351	17
α-helix	355-358	4
β-strand	360-362	3	8
α-helix	363-384	22
α-helix	391-394	4
α-helix	397-408	12
β-strand	415	1	7
α-helix	416-428	13
α-helix	432-434	3
α-helix	437-453	17
α-helix	461-474	14
α-helix	481-494	14
α-helix	497-506	10
α-helix	515-518	4
α-helix	521-523	3
β-strand	527-528	2	12
α-helix	532-537	6
α-helix	548-558	11
β-strand	574	1	13
β-strand	576	1	13
β-strand	578-581	4	12
β-strand	587-592	6	12
β-strand	597	1	14
β-strand	600-603	4	12
β-strand	614-619	6	12
β-strand	626	1	14
α-helix	635-636	2
β-strand	637-638	2	15
α-helix	645-647	3
β-strand	652-657	6	15
β-strand	663-669	7	15
α-helix	672-679	8
α-helix	681-683	3
β-strand	693-697	5	15
β-strand	703-705	3	15
α-helix	707-709	3

Chain B: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	40	1	2
α-helix	47-54	8
β-strand	60	1	2
α-helix	61-63	3
α-helix	67-69	3
α-helix	81	1
β-strand	82-83	2	16
α-helix	84-86	3
β-strand	96	1	17
β-strand	99-100	2	18
α-helix	103-112	10
α-helix	118-127	10
α-helix	133-136	4
β-strand	139	1	17
β-strand	151-155	5	19
β-strand	158-162	5	19
α-helix	164-166	3
β-strand	169-170	2	16
α-helix	173-175	3
β-strand	178-184	7	3
β-strand	188-197	10	3
β-strand	202-211	10	3
α-helix	216-218	3
α-helix	219-235	17
α-helix	241-252	12
α-helix	255-257	3

Chain C: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	83-85	3	20
β-strand	93-95	3	20
β-strand	104-110	7	20
α-helix	111-113	3
β-strand	121-128	8	20
β-strand	133-136	4	20
α-helix	138	1
α-helix	140	1
β-strand	142-143	2	20
α-helix	147-158	12
β-strand	171-172	2	21
β-strand	182	1	19
β-strand	184-189	6	17
β-strand	192-197	6	17
α-helix	198-214	17
α-helix	223-229	7
β-strand	233-234	2	18
β-strand	236	1	22
α-helix	241-250	10
β-strand	253	1	23
α-helix	315	1
β-strand	316	1	23
α-helix	317-318	2
β-strand	319-320	2	21
α-helix	321-334	14
α-helix	335-338	4
β-strand	339	1	17
α-helix	340-342	3
β-strand	347	1	24
α-helix	352-353	2
α-helix	354-359	6
α-helix	360-363	4
β-strand	369-370	2	25
β-strand	373-374	2	25
α-helix	378-380	3
β-strand	381-383	3	26
β-strand	410-412	3	26
α-helix	414-435	22
α-helix	443-446	4
β-strand	447-448	2	19
α-helix	454-457	4

Chain D: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	27
β-strand	36-38	3	28
β-strand	46-51	6	27
β-strand	55-58	4	28
β-strand	70-72	3	27
β-strand	77	1	29
β-strand	80	1	29
β-strand	81-86	6	27
α-helix	92-94	3
β-strand	96-102	7	28
α-helix	103-105	3
β-strand	107	1	22
β-strand	115-120	6	28
β-strand	128	1	30
α-helix	129-130	2
β-strand	136-141	6	31
β-strand	145-148	4	32
β-strand	152	1	30
β-strand	159-163	5	31
β-strand	167	1	31
β-strand	171-173	3	32
β-strand	177-181	5	32
β-strand	185-192	8	31
β-strand	197-199	3	31
α-helix	200-202	3
β-strand	203-208	6	31
α-helix	209-214	6
β-strand	216-219	4	24
β-strand	224-225	2	33
α-helix	229-230	2
β-strand	231-237	7	24
β-strand	246-248	3	34
α-helix	252-254	3
β-strand	258-264	7	24
β-strand	270-277	8	24
β-strand	287-292	6	34
β-strand	301-306	6	34
β-strand	308-309	2	33

Chain E: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	35
β-strand	33-35	3	36
β-strand	42-48	7	35
β-strand	52	1	37
β-strand	54	1	37
β-strand	56-61	6	36
β-strand	68-72	5	36
β-strand	76-77	2	36
α-helix	78	1
β-strand	85-90	6	35
β-strand	93-98	6	35
α-helix	103-105	3
β-strand	108-113	6	36
α-helix	120	1
β-strand	121	1	36
α-helix	122	1
β-strand	125-128	4	36

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	38
α-helix	30-32	3
β-strand	33-34	2	39
β-strand	41-48	8	38
α-helix	52-54	3
β-strand	55-62	8	39
β-strand	68-74	7	39
β-strand	81-83	3	39
β-strand	91-96	6	38
β-strand	101-106	6	38
α-helix	111-113	3
β-strand	115-125	11	39
β-strand	133-136	4	39
β-strand	140-143	4	39

Chain G: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	40
β-strand	33-35	3	41
α-helix	36-37	2
β-strand	42-48	7	40
β-strand	53	1	42
β-strand	59	1	42
β-strand	61-66	6	41
β-strand	73-77	5	41
β-strand	81-82	2	41
α-helix	83	1
β-strand	90-95	6	40
β-strand	98-103	6	40
α-helix	108-110	3
β-strand	113-118	6	41
β-strand	126	1	41
β-strand	131-133	3	41

Chain H: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	43
β-strand	34-35	2	44
β-strand	40-48	9	43
β-strand	56-62	7	45
β-strand	68-74	7	45
β-strand	81-83	3	45
β-strand	91-96	6	43
β-strand	101-107	7	43
α-helix	111-113	3
β-strand	115-122	8	45
β-strand	125	1	46
β-strand	136	1	46
β-strand	142	1	45
β-strand	144	1	43
β-strand	147-149	3	45
β-strand	150-151	2	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	767	Human cytomegalovirus (strain Merlin)	Q6SW67 (AlphaFold model)
Envelope glycoprotein L	B	protein	278	Human cytomegalovirus (strain Merlin)	F5HCH8 (AlphaFold model)
Envelope glycoprotein O	C	protein	504	Human cytomegalovirus	Q8BCU3
Isoform 3 of Platelet-derived growth factor receptor alpha	D	protein	529	Homo sapiens	P16234 (AlphaFold model)
Fab 13H11 light chain	E	protein	237	Homo sapiens
Fab 13H11 heavy chain	F	protein	250	Homo sapiens
Fab MSL-109 light chain	G	protein	257	Homo sapiens
Fab MSL-109 heavy chain	H	protein	257	Homo sapiens

Sequence of entity 1 (A), FASTA

>7LBF_1 Envelope glycoprotein H (chains A)
MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCT
YNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQ
RLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTES
HTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSI
DDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDA
ALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQ
VSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLV
RLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVH
TTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFP
DATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGI
SYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDT
QGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGTKLG
PEQKLISEEDLNSAVDGSGLNDIFEAQKIEWHENLYFQGHHHHHHHH

Sequence of entity 2 (B), FASTA

>7LBF_2 Envelope glycoprotein L (chains B)
MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVF
EGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLR
ALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLG
FELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDP
PLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR

Sequence of entity 3 (C), FASTA

>7LBF_3 Envelope glycoprotein O (chains C)
MGRKEDMRSISKLFFIISLTVLLFSIINCKVVRPPGRYWLGTVLSTIGKQKLDKFKLEIL
KQLEREPYTKYFNMTRQHVKNLTMNMTQFPQYYILAGPIRNDSITYLWFDFYSTQLRKPA
KYVYSQYNHTAKTITFRPPSCGTVPSMTCLSEMLNVSKRNDTGEQGCGNFTTFNPMFFNV
PRWNTKLYVGPTKVNVDSQTIYFLGLTALLLRYAQRNCTHSFYLVNAMSRNLFRVPKYIN
GTKLKNTMRKLKRKQAPVKEQLEKKTKKSQSTTTPYFSYTTSTALNVTTNATYRVTTSAK
RIPTSTIAYRPDSSFMKSIMATQLRDLATWVYTTLRYRNEPFCKPDRNRTAVSEFMKNTH
VLIRNETPYTIYGTLDMSSLYYNETMSVENETASDNNETTPTSPSTRFQKTFIDPLWDYL
DSLLFLDKIRNFSLQLPAYGNLTPPEHRRAVNLSTLNSLWWWLQGSENLYFQGSAWSHPQ
FEKGGGSGGGSGGGSAWSHPQFEK

Sequence of entity 4 (D), FASTA

>7LBF_4 Isoform 3 of Platelet-derived growth factor receptor alpha (chains D)
MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYP
MSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIY
VPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNG
TFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNN
EVVDLQWTYPGEVKGKGITMLEEIKVPSIKLVYTLTVPEATVKDSGDYECAARQATREVK
EMKKVTISVHEKGFIEIKPTFSQLEAVNLHEVKHFVVEVRAYPPPRISWLKNNLTLIENL
TEITTDVEKIQEIRYRSKLKLIRAKEEDSGHYTIVAQNEDAVKSYTFELLTQVPSSILDL
VDDHHGSTGGQTVRCTAEGTPLPDIEWMICKDIKKCNNETSWTILANNVSNIITEIHSRD
RSTVEGRVTFAKVEETIAVRCLAKNLLGAENRELKLVAPTLRSEDDDDK

Sequence of entity 5 (E), FASTA

>7LBF_5 Fab 13H11 light chain (chains E)
MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQ
QKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFT
FGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (F), FASTA

>7LBF_6 Fab 13H11 heavy chain (chains F)
MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWV
RQAPGQGLEWMGIIHPSSGGTSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCG
RAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCD

Sequence of entity 7 (G), FASTA

>7LBF_7 Fab MSL-109 light chain (chains G)
MKKNIAFLLASMFVFSIATNAYADIVMTQSPLSLSVTPGEPASISCRSSQSLLHTNGYNY
LDWYVQKPGQSPQLLIYLASNRASGVPDRFSGSGSGTDFTLKISRVETEDVGVYYCMQAL
QIPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDN
ALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
ECGLNDIFEAQKIEWHE

Sequence of entity 8 (H), FASTA

>7LBF_8 Fab MSL-109 heavy chain (chains H)
MKKNIAFLLASMFVFSIATNAYAEEQVLESGGGLVKPGGSLRLSCAASGFTFSPYSVFWV
RQAPGKGLEWVSSINSDSTYKYYADSVKGRFTISRDNAENSIFLQMNSLRAEDTAVYYCA
RDRSYYAFSSGSLSDYYYGLDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC
LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNH
KPSNTKVDKKVEPKSCD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

Structures of HCMV Trimer reveal the basis for receptor recognition and cell entry. Kschonsak, M., Rouge, L., Arthur, C.P. et al. Cell (2021) 184:1232. DOI 10.1016/j.cell.2021.01.036 · 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…
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…
5VOD 5.9 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

Browse structure collections

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