7RAM: Envelope glycoprotein H

Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex with PDGFRalpha. Determined by electron microscopy at 3.43 Å resolution. Released 8 Jun 2022.

Method: Electron microscopy
Resolution: 3.43 Å
Organisms: Human herpesvirus 5 strain AD169, Human betaherpesvirus 5, Homo sapiens
Chains: 4
Atoms: 12,006
Mol. weight: 220.88 kDa
Released: 8 Jun 2022

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

Secondary structure: helices and β-sheets

7RAM contains 67 α-helices and 89 β-strands across 4 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: 37 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	50-53	4	1
β-strand	57-58	2	2
β-strand	67	1	3
β-strand	70-73	4	1
β-strand	77-81	5	4
β-strand	82-84	3	3
β-strand	87-88	2	3
β-strand	91-93	3	4
α-helix	95-98	4
α-helix	105-108	4
α-helix	116-123	8
β-strand	126	1	5
α-helix	129-132	4
α-helix	134-136	3
β-strand	137-138	2	6
α-helix	149-151	3
α-helix	157-159	3
β-strand	166	1	7
β-strand	205	1	8
β-strand	212-218	7	6
β-strand	225-231	7	6
β-strand	234-240	7	6
α-helix	246	1
β-strand	247-252	6	6
β-strand	259	1	8
α-helix	265-267	3
β-strand	269-272	4	6
β-strand	277-281	5	6
β-strand	283	1	5
α-helix	284-286	3
α-helix	291-293	3
α-helix	300-303	4
α-helix	310-313	4
α-helix	314-318	5
α-helix	319-328	10
α-helix	337-353	17
α-helix	356-358	3
α-helix	364-384	21
α-helix	389-391	3
α-helix	393-395	3
α-helix	398-409	12
α-helix	411-413	3
β-strand	416	1	7
α-helix	417-430	14
α-helix	432-434	3
α-helix	438-440	3
α-helix	442-454	13
α-helix	464-472	9
α-helix	483-494	12
α-helix	498-507	10
α-helix	516-519	4
α-helix	533-537	5
α-helix	544-545	2
α-helix	549-559	11
α-helix	564-566	3
α-helix	579-582	4
β-strand	583-584	2	9
β-strand	588-590	3	9
β-strand	592-593	2	10
β-strand	602-604	3	10
α-helix	609-611	3
β-strand	615-617	3	10
β-strand	619-620	2	9
β-strand	634	1	10
β-strand	653-658	6	11
β-strand	668-670	3	11
α-helix	673-678	6
β-strand	694-698	5	11
β-strand	704-706	3	11

Chain B: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	39	1	2
α-helix	47-55	9
β-strand	60-61	2	2
α-helix	84-86	3
β-strand	96	1	12
β-strand	99-100	2	13
α-helix	103-112	10
α-helix	118-126	9
α-helix	133-136	4
β-strand	139	1	12
β-strand	151-155	5	14
β-strand	158-162	5	14
α-helix	173-175	3
β-strand	178-184	7	4
β-strand	188-195	8	4
β-strand	204-211	8	4
β-strand	212	1	15
β-strand	215	1	15
α-helix	216-218	3
α-helix	219-235	17
α-helix	242-251	10
α-helix	259-261	3

Chain C: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	85-87	3	16
β-strand	95-97	3	16
β-strand	106-111	6	16
α-helix	113-116	4
β-strand	124-130	7	16
β-strand	135-144	10	16
α-helix	149-161	13
β-strand	173-174	2	17
β-strand	184	1	14
β-strand	186-191	6	12
β-strand	194-199	6	12
α-helix	200-215	16
α-helix	225-230	6
β-strand	235-236	2	13
β-strand	238	1	18
α-helix	243-251	9
β-strand	321-322	2	17
α-helix	323-337	15
α-helix	338-340	3
β-strand	341	1	12
α-helix	342-345	4
α-helix	354-355	2
α-helix	356-359	4
α-helix	362-365	4
β-strand	371	1	19
β-strand	376	1	19
α-helix	413-434	22
α-helix	435-437	3
α-helix	442-444	3
β-strand	446-447	2	14
α-helix	452-455	4
α-helix	460-462	3

Chain D: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
β-strand	29-30	2	20
β-strand	36-38	3	21
β-strand	44-51	8	20
β-strand	55-58	4	21
β-strand	69	1	20
β-strand	72-74	3	20
β-strand	81-88	8	20
α-helix	92-94	3
β-strand	96-102	7	21
β-strand	107	1	18
β-strand	116-120	5	21
β-strand	128	1	22
β-strand	138-140	3	23
β-strand	152	1	22
β-strand	159-160	2	24
β-strand	171-173	3	25
β-strand	177-179	3	25
β-strand	185-187	3	23
β-strand	190-193	4	24
β-strand	196-199	4	24
β-strand	203-207	5	23
α-helix	210-213	4
β-strand	216-219	4	26
β-strand	224-226	3	27
β-strand	231-237	7	26
β-strand	245-248	4	28
α-helix	252-254	3
β-strand	258-264	7	26
β-strand	270-277	8	26
β-strand	286-293	8	28
β-strand	300-307	8	28
β-strand	308-310	3	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	706	Human herpesvirus 5 strain AD169	P12824
Envelope glycoprotein L	B	protein	242	Human herpesvirus 5 strain AD169	P16832
Envelope glycoprotein O	C	protein	463	Human betaherpesvirus 5	Q8AZ32
Platelet-derived growth factor receptor alpha	D	protein	530	Homo sapiens	P16234 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7RAM_1 Envelope glycoprotein H (chains A)
LLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAG
PLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSLGQQPTTVPPPI
DLSIPHVWMPPQTTPHDWKGSHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLM
DELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLV
LVKKAQLNRHSYLKDSDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVE
MAFAYALALFAAARQEEAGTEISIPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTA
VDLAKRALWTPDQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFALQLHKTHLASFL
SAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLY
TPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFS
ALTVSEHVSYVVTNQYLIKGISYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITAA
LNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLK
NGTVLEVTDVVVDATDSRGSLVPRGSSAWSHPQFEKAGHHHHHHHH

Sequence of entity 2 (B), FASTA

>7RAM_2 Envelope glycoprotein L (chains B)
PTAAEKVPAECPELTRRCLLGEVFQGDKYESWLRPLVNVTRRDGPLSQLIRYRPVTPEAA
NSVLLDDAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVD
DLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAP
EGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVD
AR

Sequence of entity 3 (C), FASTA

>7RAM_3 Envelope glycoprotein O (chains C)
MGRKGEMRGVFNLFFLMSLTFLLFSFINCRAAVRLSVGRYWSGKVLSTIGKQRLDKFKLE
ILKQLEKDIYTKYFNMTRQHIKNLTMNMTEFPRYYILAGPIQNNSVTYLWFDFYSTQLRK
PAKYVFSEYNHTAKTITFRPPSCGTVPSMTCLSEMLNVSKRNDTGEQGCGNFTTFNPMFF
NVPRWNTKLYVGSKKVNVDSQTIYFLGLTALLLRYAQRNCTHSFYLVNAMSRNLFRVPKY
INGTKLKNTMRKLKRKQAPVKEQSEKKSKKSQSTTTPYSPYTTSTALNVTTNATYSVTTT
ARRVSTSTIAYRPDSSFMKSIMTTQLRDLATWVYTTLRYRQNPFCESSRNRTAVSEFMKN
THVLIRNETPYTIYGTLDMSSLYYNETMFVENKTASETTPTSPSTGFQRTFIDPLWDYLD
SLLFLDEIRNFSLQSPTYGNLTPPEHRRAVNLSTLNSLWWWLQ

Sequence of entity 4 (D), FASTA

>7RAM_4 Platelet-derived growth factor receptor alpha (chains D)
MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYP
MSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIY
VPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNG
TFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNN
EVVDLQWTYPGEVKGKGITMLEEIKVPSIKLVYTLTVPEATVKDSGDYECAARQATREVK
EMKKVTISVHEKGFIEIKPTFSQLEAVNLHEVKHFVVEVRAYPPPRISWLKNNLTLIENL
TEITTDVEKIQEIRYRSKLKLIRAKEEDSGHYTIVAQNEDAVKSYTFELLTQVPSSILDL
VDDHHGSTGGQTVRCTAEGTPLPDIEWMICKDIKKCNNETSWTILANNVSNIITEIHPRD
RSTVEGRVTFAKVEETIAVRCLAKNLLGAENRELKLVAPTLRSEENLYFQ

Primary citation

Cryo-Electron Microscopy Structure and Interactions of the Human Cytomegalovirus gHgLgO Trimer with Platelet-Derived Growth Factor Receptor Alpha. Liu, J., Vanarsdall, A., Chen, D.H. et al. mBio (2021) 12:e0262521-e0262521. DOI 10.1128/mBio.02625-21 · PubMed

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

8TCO 2.8 Å, HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
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

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