7RKM: CX3CL1-US28-Gi-scFv16 in C-state

Structure of CX3CL1-US28-Gi-scFv16 in C-state. Determined by electron microscopy at 3.5 Å resolution. Released 26 Jan 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Mus musculus, Human betaherpesvirus 5
Chains: 6
Atoms: 9,491
Mol. weight: 165.23 kDa
Ligands: CLR
Released: 26 Jan 2022

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

Secondary structure: helices and β-sheets

7RKM contains 35 α-helices and 65 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	322	1	1
α-helix	331-351	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-263	5	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	27-29	3
α-helix	30-42	13
α-helix	45-47	3
α-helix	53-55	3

Chain D: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
α-helix	53-55	3
β-strand	58-60	3	10
β-strand	65	1	9
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	111	1	10
β-strand	115-119	5	10
β-strand	128-130	3	11
β-strand	134-136	3	12
β-strand	143-149	7	11
β-strand	154	1	13
β-strand	160	1	13
β-strand	162-167	6	12
β-strand	174-178	5	12
β-strand	182-183	2	12
α-helix	184	1
β-strand	191-195	5	11
β-strand	199-204	6	11
β-strand	214-219	6	12
β-strand	231-234	4	12

Chain L: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	10-11	2	14
β-strand	24-29	6	15
β-strand	39-43	5	15
β-strand	48-51	4	15
α-helix	57-66	10

Chain R: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	14
α-helix	26-58	33
α-helix	67-94	28
α-helix	104-133	30
α-helix	141-157	17
α-helix	160-163	4
β-strand	167-168	2	16
β-strand	173-174	2	16
α-helix	184-193	10
α-helix	194-198	5
α-helix	199-217	19
α-helix	223-255	33
α-helix	264-291	28
α-helix	296-303	8

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 betaherpesvirus 5	P69332

Sequence of entity 1 (A), FASTA

>7RKM_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7RKM_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

>7RKM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>7RKM_4 Antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (L), FASTA

>7RKM_5 Fractalkine (chains L)
QHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 6 (R), FASTA

>7RKM_6 G-protein coupled receptor homolog US28 (chains R)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

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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