7KBB: HCMV pentamer bound by Fabs 2-18 and 8I21

Cryo-EM structure of the HCMV pentamer bound by Fabs 2-18 and 8I21. Determined by electron microscopy at 4.02 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 4.02 Å
Organisms: Homo sapiens, Human cytomegalovirus
Chains: 7
Atoms: 6,422
Mol. weight: 149.16 kDa
Released: 11 Aug 2021

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

Secondary structure: helices and β-sheets

7KBB contains 25 α-helices and 63 β-strands across 7 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	67-71	5	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-97	10	2
α-helix	100A-100C	3
β-strand	102-103	2	2
β-strand	107-111	5	2

Chain B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	11-12	2	4
β-strand	19-25	7	3
β-strand	29	1	5
β-strand	33-38	6	4
β-strand	44-49	6	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-67	6	3
β-strand	68	1	5
β-strand	70-75	6	3
α-helix	80-82	3
β-strand	84-90	7	4
α-helix	96	1
β-strand	97	1	2
β-strand	98	1	4
β-strand	102-105	4	4

Chain C: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	86-91	6
α-helix	94-96	3
α-helix	99-100	2
β-strand	101-103	3	6
β-strand	109-111	3	6
α-helix	112-113	2
β-strand	121-122	2	6
β-strand	125	1	7
β-strand	130-131	2	8
α-helix	146-154	9

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	49-54	6
α-helix	62-65	4
α-helix	68-70	3
β-strand	71-78	8	9
α-helix	81-83	3
β-strand	87-93	7	9
β-strand	98-102	5	9
α-helix	105-117	13
α-helix	120-130	11
α-helix	141-150	10
β-strand	154-165	12	8
β-strand	168-182	15	8
β-strand	188-198	11	8
β-strand	212	1	7

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
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	97-98	2	8
β-strand	107-114	8	8
β-strand	117-126	10	8

Chain H: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	93-103	11	12
β-strand	106-112	7	12
β-strand	116-117	2	12
β-strand	119-120	2	11

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
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	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	99	1	14
β-strand	103-107	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-18 Fab Heavy Chain	A	protein	240	Homo sapiens
2-18 Fab Light Chain	B	protein	214	Homo sapiens
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)
8I21 Fab Heavy Chain	H	protein	234	Homo sapiens
8I21 Fab Light Chain	L	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>7KBB_1 2-18 Fab Heavy Chain (chains A)
EVQLVQSGGGLVQPGGSLRVSCAASGFSFSDHDMDWVRQAPGKGFEWVGRSRNKDYSSTT
EYAASVRGRFTISRHTSEDLLYLELNTVKTEDTAVYFCARGPHHSDRSGYYGGTFDIWGQ
GTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 2 (B), FASTA

>7KBB_2 2-18 Fab Light Chain (chains B)
DIQMTQSPSSVSASVGDRVIITCRASQGISSWLAWYQQKPGRAPRLLIYDASTLESGVPS
RFSGRGSGTEFTLTINSLQPEDFATYYCQQGNMFPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>7KBB_3 Envelope protein UL128 (chains C)
EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQ
VVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLD
QYLESVKKHKRLDVCRAKMGYMLQ

Sequence of entity 4 (D), FASTA

>7KBB_4 Envelope glycoprotein UL130 (chains D)
SPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRN
ETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAK
IFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYT
FCTHPNLIV

Sequence of entity 5 (E), FASTA

>7KBB_5 UL131A (chains E)
QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLK
RINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

Sequence of entity 6 (H), FASTA

>7KBB_6 8I21 Fab Heavy Chain (chains H)
LVELVESGGGVVQPGRSLRLSCAASGFTFSSDGMHWVRQSPGRGLEWVAFISSDGSTPYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYFCAKDWALFRWLRTFDHWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 7 (L), FASTA

>7KBB_7 8I21 Fab Light Chain (chains L)
ETVMTQSPATLSVSPGGRATLSCRASQSVGINLAWYQQKPGQAPRLLIYGASTRASGFPA
RFSGSGSGTEFTLTITSLQSEDFAVYYCQQYNDWPPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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
7M22 3.65 Å, Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2
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…
5VOD 5.9 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

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