9DIY: Envelope glycoprotein H

Local Cryo-EM structure of HCMV gH/UL116 interaction. Determined by electron microscopy at 5.36 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 5.36 Å
Organism: Human betaherpesvirus 5
Chains: 3
Atoms: 4,625
Mol. weight: 146.86 kDa
Ligands: NAG
Released: 20 Nov 2024

Explore 9DIY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DIY contains 27 α-helices and 35 β-strands across 3 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: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
α-helix	62-64	3
α-helix	65-69	5
α-helix	70-71	2
β-strand	78-84	7	1
β-strand	87-92	6	1
α-helix	95-98	4
α-helix	101-106	6
α-helix	107-109	3
α-helix	116-123	8
β-strand	126	1	2
α-helix	129-133	5
α-helix	190-193	4
β-strand	195-198	4	3
β-strand	208-211	4	3
β-strand	214-215	2	4
β-strand	226-231	6	4
β-strand	234-239	6	4
β-strand	247-252	6	4
β-strand	277-281	5	4
β-strand	283	1	2
α-helix	284-288	5
α-helix	292-294	3
α-helix	306-307	2

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	40	1	5
β-strand	43	1	6
α-helix	47-50	4
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	64-65	2	7
β-strand	68	1	7
β-strand	76-83	8	6
β-strand	91-96	6	6
β-strand	102-105	4	6
β-strand	115-119	5	7
β-strand	126-130	5	7
α-helix	135-137	3
β-strand	139-146	8	6
β-strand	150	1	5
β-strand	151-160	10	6
β-strand	162-167	6	8
α-helix	172-174	3
β-strand	186	1	9
β-strand	188	1	6
α-helix	192-194	3
β-strand	195-203	9	8
β-strand	206-213	8	8
α-helix	224-227	4
α-helix	235-238	4
β-strand	242	1	9
β-strand	248	1	8

Chain C: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	210-211	2	1
α-helix	219-221	3
α-helix	233-235	3
α-helix	239-241	3
β-strand	244-248	5	1
β-strand	260-264	5	1
β-strand	269-272	4	1
α-helix	275-288	14
α-helix	291-294	4
α-helix	297-301	5
α-helix	302-304	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	680	Human betaherpesvirus 5	P12824
UL116	C	protein	332	Human betaherpesvirus 5	Q6SW34 (AlphaFold model)
Protein UL141	B	protein	273	Human betaherpesvirus 5	Q6RJQ3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DIY_1 Envelope glycoprotein H (chains A)
ASEALDPHAFHLLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYY
VFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSL
GQQPTTVPPPIDLSIPHVWMPPQTTPHDWKGSHTTSGLHRPHFNQTCILFDGHDLLFSTV
TPCLHQGFYLMDELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFI
LRQTEKHELLVLVKKTQLNRHSYLKDSDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSG
RCQMLDRRTVEMAFAYALALFAAARQEEAGTEISIPRALDRQAALLQIQEFMITCLSQTP
PRTTLLLYPTAVDLAKRALWTPDQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFAL
QLHKTHLASFLSAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLA
HPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQPSTLETFPD
LFCLPLGESFSALTVSEHVSYVVTNQYLIKGISYPVSTTVVGQSLIITQTDSQSKCELTR
NMHTTHSITAALNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVS
SPRTHYLMLLKNGTVLEVTD

Sequence of entity 2 (C), FASTA

>9DIY_2 UL116 (chains C)
VETNATTVTSTTAAAATTNTTVATTGTTTTSPNVTSTTSNTVITPTTVSSVSNLTSSATS
IPISTSTVSGTRNTRNNNTTTIGTNVTSPSPSVSILTTVTPAATSTTSNNGDVTSDYTPT
FDLENITTTRAPTRPPAQDLCSHNLSIILYEEESQSSVDIAVDEEEPELEDDDEYDELWF
PLYFEAECNLNYTLQYVNHSCDYSVRQSSVSFPPWRDIDSVTFVPRNLSNCSAHGLAVIV
AGNQTWYVNPFSLAHLLDAIYNVLGIEDLSANFRRQLAPYRHTLIVPQTGGSGGSGSDDD
DKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 3 (B), FASTA

>9DIY_3 Protein UL141 (chains B)
SFPFATADIAEKMWAENYETTSPAPVLVAEGEQVTIPCTVMTHSWPMVSIRARFCRSHDG
SDELILDAVKGHRLMNGLQYRLPYATWNFSQLHLGQIFSLTFNVSTDTAGMYECVLRNYS
HGLIMQRFVILTQLETLSRPDEPCCTPALGRYSLGDQIWSPTPWRLRNHDCGMYRGFQRN
YFYIGRADAEDCWKPACPDEEPDRCWTVIQRYRLPGDCYRSQPHPPKFLPVTPAPPADID
TGMSPWATRGGSGGGSLEVLFQGPGHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

A noncanonical glycoprotein H complex enhances cytomegalovirus entry. Norris, M.J., Henderson, L.A., Siddiquey, M.N.A. et al. bioRxiv (2024). DOI 10.1101/2024.10.13.617647 · 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
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

Browse structure collections

About this viewer

MolViewer shows 9DIY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.