7RKF: CX3CL1-US28-G11iN18-scFv16 in TL-state

Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state. Determined by electron microscopy at 4.0 Å resolution. Released 26 Jan 2022.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: Homo sapiens, Mus musculus, Human cytomegalovirus
Chains: 6
Atoms: 10,563
Mol. weight: 166.47 kDa
Ligands: GDP, NAG
Released: 26 Jan 2022

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

Secondary structure: helices and β-sheets

7RKF contains 52 α-helices and 68 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: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-29	21
β-strand	33-39	7	1
α-helix	46-53	8
α-helix	54-58	5
α-helix	63-67	5
α-helix	70-90	21
α-helix	98-102	5
α-helix	105-108	4
α-helix	120-130	11
α-helix	133-140	8
α-helix	149-151	3
α-helix	152-155	4
α-helix	158-162	5
α-helix	170-173	4
β-strand	185-190	6	1
β-strand	193-198	6	1
α-helix	208-211	4
α-helix	212-214	3
β-strand	219-225	7	1
α-helix	227-230	4
α-helix	241-254	14
α-helix	256-258	3
β-strand	262-268	7	1
α-helix	270-274	5
α-helix	277-279	3
α-helix	282-285	4
α-helix	296-309	14
β-strand	319-322	4	1
α-helix	329-343	15

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
α-helix	30-33	4
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
α-helix	129-131	3
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	251-254	4	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	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	30-43	14

Chain D: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
β-strand	6	1	10
β-strand	11-12	2	11
β-strand	17-23	7	10
β-strand	25	1	9
α-helix	29-31	3
β-strand	35-39	5	12
β-strand	45-51	7	12
α-helix	53-55	3
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-96	5	12
β-strand	97	1	13
β-strand	111	1	13
β-strand	115-117	3	12
β-strand	118-119	2	11
α-helix	126-128	3
β-strand	129	1	14
β-strand	134-136	3	15
β-strand	143-147	5	16
β-strand	148	1	14
β-strand	154	1	17
β-strand	160	1	17
β-strand	162-166	5	18
β-strand	174-178	5	18
β-strand	193-195	3	16
β-strand	200-204	5	16
β-strand	214	1	15
β-strand	217-219	3	18
α-helix	225	1
β-strand	227	1	18
β-strand	232-234	3	15

Chain L: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	15-16	2
α-helix	21-23	3
β-strand	24-27	4	19
β-strand	39-43	5	19
β-strand	48-51	4	19
α-helix	56-66	11

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-57	32
α-helix	67-84	18
α-helix	86-94	9
α-helix	99-101	3
α-helix	104-135	32
α-helix	141-158	18
α-helix	160-162	3
β-strand	169	1	20
β-strand	172	1	20
α-helix	184-193	10
α-helix	194-198	5
α-helix	199-217	19
α-helix	223-255	33
α-helix	263-280	18
α-helix	281-286	6
α-helix	287-291	5
α-helix	296-309	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein subunit alpha-11	A	protein	352	Homo sapiens	P29992 (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

>7RKF_1 Guanine nucleotide-binding protein subunit alpha-11 (chains A)
GCTLSAEDKAAVERSKMIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGY
SEEDKRGFTKLVYQNIFTAMQAMIRAMETLKILYKYEQNKANALLIREVDVEKVTTFEHQ
YVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTT
GIIEYPFDLENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENR
MEESKALFRTIITYPWFQNSSVILFLNKKDLLEDKILYSHLVDYFPEFDGPQRDAQAARE
FILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV

Sequence of entity 2 (B), FASTA

>7RKF_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

>7RKF_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>7RKF_4 Antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (L), FASTA

>7RKF_5 Fractalkine (chains L)
QHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 6 (R), FASTA

>7RKF_6 G-protein coupled receptor homolog US28 (chains R)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	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 P29992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
9P87 2.8 Å, NTSR1-G11-NTS(8-13) Complex in the Canonical, AHD Partially Closed State (C-P-Closed-Apo)
9UCP 2.88 Å, cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein…
7XXH 2.9 Å, Cryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11
9P86 2.9 Å, NTSR1-G11-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
9P88 2.9 Å, NTSR1-G11-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
6OIJ 3.3 Å, Muscarinic acetylcholine receptor 1-G11 protein complex
9UAP 3.62 Å, cryo-EM structure of ligand-free active-state M1 muscarinic acetylcholine receptor with…
7TRY 3.7 Å, Cryo-EM structure of corticotropin releasing factor receptor 2 bound to Urocortin 1 and…
9P8A 3.7 Å, NTSR1-G11-NTS(8-13) GTP-Bound Complex in the Canonical, AHD Closed State 3DVA Separated…
9P89 3.9 Å, NTSR1-G11-NTS(8-13) GTP-Bound Complex in the Canonical, AHD Closed State 3DVA Separated…

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