7M22: HCMV pentamer bound by human neuropilin 2

Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2. Determined by electron microscopy at 3.65 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 3.65 Å
Organisms: Human cytomegalovirus, Homo sapiens
Chains: 4
Atoms: 6,042
Mol. weight: 117.36 kDa
Ligands: NAG, CA
Released: 11 Aug 2021

Explore 7M22 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M22 contains 27 α-helices and 55 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 C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	39-40	2
β-strand	45-48	4	1
β-strand	54-57	4	1
β-strand	63-65	3	1
α-helix	72-80	9
α-helix	81-83	3
α-helix	86-91	6
α-helix	94-96	3
β-strand	101-103	3	2
β-strand	109-111	3	2
α-helix	112-113	2
α-helix	118-120	3
β-strand	121-122	2	2
β-strand	125	1	3
β-strand	130-133	4	4

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	105-117	13
α-helix	120-128	9
β-strand	138	1	5
α-helix	141-148	8
β-strand	155-165	11	4
β-strand	168-182	15	4
β-strand	188-198	11	4
β-strand	212	1	3

Chain E: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	36-40	5
α-helix	42-45	4
α-helix	46-68	23
α-helix	74-77	4
α-helix	82-94	13
β-strand	97-98	2	4
β-strand	107-113	7	4
β-strand	117-126	10	4
β-strand	127	1	5

Chain N: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	152-153	2	6
β-strand	158-161	4	7
α-helix	168-170	3
β-strand	174-180	7	6
α-helix	181-182	2
β-strand	186-195	10	7
β-strand	196	1	8
β-strand	212-216	5	6
α-helix	224	1
β-strand	225-229	5	6
β-strand	231	1	8
α-helix	234-237	4
β-strand	238-240	3	7
β-strand	244-250	7	6
β-strand	259-267	9	7
β-strand	279-280	2	9
α-helix	290-292	3
β-strand	293-295	3	9
α-helix	306-309	4
β-strand	310	1	9
β-strand	329-345	17	9
β-strand	347-348	2	10
β-strand	355-356	2	10
β-strand	358-366	9	9
β-strand	373-374	2	9
β-strand	376	1	11
β-strand	381	1	11
α-helix	382	1
β-strand	384-385	2	9
β-strand	394-414	21	9
β-strand	421-427	7	9
α-helix	429-431	3
β-strand	436-437	2	12
α-helix	447-449	3
β-strand	450-452	3	12
α-helix	462-465	4
β-strand	474	1	13
α-helix	481-482	2
β-strand	488-504	17	12
β-strand	506	1	14
β-strand	519	1	14
β-strand	521-529	9	12
β-strand	536-537	2	12
β-strand	539	1	15
β-strand	546	1	15
β-strand	549-550	2	12
β-strand	559-578	20	12
β-strand	585	1	13
β-strand	586-592	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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)
Neuropilin-2	N	protein	581	Homo sapiens	O60462 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7M22_1 Envelope protein UL128 (chains C)
EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQ
VVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLD
QYLESVKKHKRLDVCRAKMGYMLQ

Sequence of entity 2 (D), FASTA

>7M22_2 Envelope glycoprotein UL130 (chains D)
SPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRN
ETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAK
IFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYT
FCTHPNLIV

Sequence of entity 3 (E), FASTA

>7M22_3 UL131A (chains E)
QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLK
RINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

Sequence of entity 4 (N), FASTA

>7M22_4 Neuropilin-2 (chains N)
QPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHD
CKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQGAGFSLRYEIF
KTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPLQ
VGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSA
RYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNL
DSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHK
VFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLS
GLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVI
IQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRR
FDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTGSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	1

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 P16837), best resolution first:

5VOB 3.02 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
8TEA 3.4 Å, HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
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

Browse structure collections

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