7O7F: PDB entry 7O7F

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist. Determined by electron microscopy at 3.15 Å resolution. Released 30 Jun 2021.

Method: Electron microscopy
Resolution: 3.15 Å
Organisms: Homo sapiens, Bos taurus, Mus musculus
Chains: 7
Atoms: 11,170
Mol. weight: 184.44 kDa
Released: 30 Jun 2021

Explore 7O7F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O7F contains 47 α-helices and 87 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	33-39	7	1
α-helix	46-53	8
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	213-215	3
β-strand	220-226	7	1
α-helix	242-254	13
α-helix	262	1
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	1
α-helix	330-351	22

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
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	88-94	7	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
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	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	217-222	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	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	336-339	4	2

Chain C: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-57	32
α-helix	64-90	27
α-helix	98-131	34
α-helix	133-139	7
α-helix	142-164	23
β-strand	167	1	9
β-strand	170-171	2	10
β-strand	176-177	2	10
β-strand	180	1	9
α-helix	184-199	16
α-helix	200-204	5
α-helix	205-223	19
α-helix	229-259	31
α-helix	262-264	3
α-helix	269-298	30
α-helix	303-313	11

Chain F: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	22-23	2
β-strand	24-25	2	17
β-strand	33	1	18
β-strand	39-43	5	19
β-strand	44-45	2	17
β-strand	50	1	20
β-strand	56	1	20
β-strand	58-63	6	21
β-strand	70-74	5	21
β-strand	78-79	2	21
α-helix	80	1
β-strand	87-92	6	19
β-strand	95-100	6	19
α-helix	105-107	3
β-strand	109-115	7	21
β-strand	123	1	21
β-strand	127-129	3	21
β-strand	131	1	18
β-strand	136	1	22
β-strand	139-143	5	23
α-helix	144-146	3
α-helix	147-151	5
β-strand	154-164	11	23
β-strand	165	1	22
β-strand	170-175	6	24
β-strand	178-180	3	24
β-strand	184-188	5	23
α-helix	189-192	4
β-strand	198-207	10	23
α-helix	208-212	5
β-strand	216-222	7	24
α-helix	229	1
β-strand	230-235	6	24

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	11-26	16
α-helix	33-48	16
α-helix	59-61	3

Chain H: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	12
β-strand	29-31	3	13
β-strand	36-44	9	12
α-helix	48-50	3
β-strand	52-58	7	13
β-strand	64-70	7	13
α-helix	72-74	3
β-strand	77-79	3	13
β-strand	87-92	6	12
β-strand	97-103	7	12
α-helix	107-109	3
β-strand	111-118	8	13
β-strand	129-130	2	13
β-strand	134-138	5	13
α-helix	141-143	3
β-strand	144	1	14
β-strand	147-151	5	15
β-strand	162-172	11	15
β-strand	173	1	14
β-strand	178-181	4	16
α-helix	182-184	3
β-strand	190-192	3	15
α-helix	193-195	3
β-strand	196-198	3	15
β-strand	201-211	11	15
β-strand	221-226	6	16
β-strand	231-236	6	16

Chain I: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	21-23	3
β-strand	24-29	6	11
α-helix	30-31	2
β-strand	39-43	5	11
β-strand	48-49	2	11
α-helix	56-65	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
C-C chemokine receptor type 5	C	protein	372	Homo sapiens	P51681 (AlphaFold model)
Guanine nucleotide-binding protein G(T) subunit gamma-T1	G	protein	74	Bos taurus	P02698 (AlphaFold model)
C-C motif chemokine 5	I	protein	69	Homo sapiens	P13501
Fab antibody fragment heavy chain	H	protein	221	Mus musculus
Fab antibody fragment light chain	F	protein	217	Mus musculus

Sequence of entity 1 (A), FASTA

>7O7F_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7O7F_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7O7F_3 C-C chemokine receptor type 5 (chains C)
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSS
HFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTI
MIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFV
GEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTGEQEISVGLGVAGLEVL
FQGPDYKDDDDK

Sequence of entity 4 (G), FASTA

>7O7F_4 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPED
KNPFKELKGGCVIS

Sequence of entity 5 (I), FASTA

>7O7F_5 C-C motif chemokine 5 (chains I)
QGPPGDIVLACCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVR
EYINSLEMS

Sequence of entity 6 (H), FASTA

>7O7F_6 Fab antibody fragment heavy chain (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQS
GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS

Sequence of entity 7 (F), FASTA

>7O7F_7 Fab antibody fragment light chain (chains F)
DIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLA
SGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Primary citation

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist. Isaikina, P., Tsai, C.J., Dietz, N. et al. Sci Adv (2021) 7. DOI 10.1126/sciadv.abg8685 · PubMed

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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