7RKN: CX3CL1-US28-Gi-scFv16 in OC-state

Structure of CX3CL1-US28-Gi-scFv16 in OC-state. Determined by electron microscopy at 3.6 Å resolution. Released 26 Jan 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Mus musculus, Human cytomegalovirus
Chains: 6
Atoms: 9,393
Mol. weight: 164.84 kDa
Released: 26 Jan 2022

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

Secondary structure: helices and β-sheets

7RKN contains 34 α-helices and 74 β-strands across 6 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	34-38	5	1
α-helix	46-50	5
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	201-203	3
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-222	3	1
β-strand	225-226	2	2
α-helix	242-254	13
β-strand	263-266	4	1
β-strand	268-269	2	2
α-helix	271-279	9
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-321	3	1
α-helix	329-351	23

Chain B: 2 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	6-23	18
α-helix	30-33	4
β-strand	47	1	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
β-strand	102-105	4	5
β-strand	111-115	5	5
β-strand	120	1	6
β-strand	122-125	4	5
β-strand	134-137	4	5
β-strand	140	1	6
β-strand	149-151	3	7
β-strand	156-159	4	7
β-strand	166-170	5	7
β-strand	178-180	3	7
β-strand	189-192	4	8
β-strand	198-202	5	8
β-strand	208-212	5	8
β-strand	218-221	4	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	260-264	5	9
β-strand	273-278	6	10
β-strand	284	1	11
β-strand	285-289	5	10
β-strand	294-295	2	10
β-strand	298	1	11
β-strand	315-317	3	12
β-strand	320	1	13
β-strand	327	1	13
β-strand	330-331	2	12
β-strand	339	1	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2

Chain D: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	14
β-strand	6	1	15
β-strand	10-12	3	16
β-strand	17-23	7	15
β-strand	25	1	14
α-helix	29-31	3
β-strand	35-39	5	16
β-strand	45-50	6	16
β-strand	51	1	17
α-helix	53-55	3
β-strand	58	1	17
β-strand	68-73	6	15
β-strand	78-84	7	15
α-helix	88-90	3
β-strand	92-97	6	16
β-strand	111	1	16
β-strand	115-119	5	16
β-strand	136	1	18
β-strand	143-148	6	19
β-strand	162-166	5	20
β-strand	167	1	21
β-strand	174-178	5	20
β-strand	185	1	22
β-strand	187	1	22
β-strand	193-196	4	19
β-strand	199-204	6	19
β-strand	214	1	21
β-strand	215	1	23
β-strand	218-219	2	20
α-helix	225	1
β-strand	231	1	23
β-strand	234	1	18

Chain L: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	24
β-strand	39-42	4	24
β-strand	48-51	4	24
α-helix	57-67	11

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-56	31
α-helix	57-61	5
α-helix	67-92	26
α-helix	104-130	27
α-helix	131-135	5
α-helix	141-163	23
β-strand	167-168	2	25
β-strand	173-174	2	25
α-helix	184-193	10
α-helix	194-198	5
α-helix	199-215	17
α-helix	223-239	17
α-helix	242-256	15
α-helix	263-291	29
α-helix	296-305	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	353	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	67	Homo sapiens	P59768 (AlphaFold model)
Antibody fragment scFv16	D	protein	256	Mus musculus
Fractalkine	L	protein	91	Homo sapiens	P78423 (AlphaFold model)
G-protein coupled receptor homolog US28	R	protein	362	Human cytomegalovirus	P69332

Sequence of entity 1 (A), FASTA

>7RKN_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7RKN_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7RKN_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>7RKN_4 Antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (L), FASTA

>7RKN_5 Fractalkine (chains L)
QHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 6 (R), FASTA

>7RKN_6 G-protein coupled receptor homolog US28 (chains R)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Primary citation

Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins. Tsutsumi, N., Maeda, S., Qu, Q. et al. Sci Adv (2022) 8:eabl5442. DOI 10.1126/sciadv.abl5442

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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