6LFM: Class A GPCR

Cryo-EM structure of a class A GPCR. Determined by electron microscopy at 3.5 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 7
Atoms: 10,181
Mol. weight: 171.96 kDa
Ligands: CLR
Released: 2 Sept 2020

Explore 6LFM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LFM contains 47 α-helices and 76 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-38	5	1
α-helix	46-49	4
β-strand	184-187	4	1
β-strand	190	1	2
β-strand	195	1	2
β-strand	196-201	6	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-221	2	1
β-strand	223-226	4	3
α-helix	227-230	4
α-helix	232-234	3
α-helix	242-254	13
β-strand	265-269	5	3
α-helix	271-278	8
α-helix	296-307	12
β-strand	320-323	4	3
α-helix	330-351	22

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	91-94	4	5
β-strand	103-105	3	6
β-strand	111-114	4	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-153	8	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	176-180	5	7
α-helix	186-187	2
β-strand	189-192	4	8
β-strand	198-202	5	8
β-strand	208-212	5	8
β-strand	220-222	3	8
β-strand	229-234	6	9
β-strand	241-245	5	9
β-strand	250-253	4	9
β-strand	260-264	5	9
β-strand	273-278	6	10
α-helix	279	1
α-helix	280-282	3
β-strand	284-289	6	10
β-strand	295-298	4	10
β-strand	315-317	3	4
β-strand	320	1	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-22	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain D: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	24-28	5	11
β-strand	38-40	3	11
β-strand	41-42	2	12
β-strand	48-49	2	12
α-helix	58-69	12

Chain E: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	11
β-strand	38-43	6	11
β-strand	49-50	2	11
α-helix	56-59	4
α-helix	61-69	9

Chain R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-59	13
α-helix	61-74	14
α-helix	82-97	16
α-helix	101-110	10
α-helix	116-135	20
α-helix	140-146	7
α-helix	156-160	5
α-helix	162-176	15
α-helix	178-181	4
β-strand	184-185	2	13
β-strand	197-198	2	13
α-helix	208-213	6
α-helix	215-218	4
α-helix	221-228	8
α-helix	231-240	10
α-helix	246-279	34
α-helix	286-314	29
α-helix	319-331	13

Chain S: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	14
β-strand	7	1	15
β-strand	17-21	5	15
β-strand	24-25	2	14
α-helix	29-31	3
β-strand	35-39	5	16
β-strand	45-50	6	16
α-helix	53-55	3
β-strand	60	1	16
β-strand	68-73	6	15
β-strand	78-84	7	15
α-helix	88-90	3
β-strand	92-95	4	16
β-strand	97	1	17
β-strand	111	1	17
β-strand	115-117	3	16
β-strand	129	1	18
β-strand	135-136	2	19
β-strand	144-148	5	18
β-strand	154	1	20
β-strand	160	1	20
β-strand	162-163	2	21
β-strand	165-166	2	22
β-strand	167	1	19
β-strand	174-175	2	22
β-strand	177-178	2	23
β-strand	182-183	2	23
β-strand	191-195	5	18
β-strand	199-204	6	18
α-helix	209-211	3
β-strand	213-215	3	19
β-strand	218-219	2	21
α-helix	226	1
β-strand	227	1	21
α-helix	228	1
α-helix	230	1
β-strand	231-234	4	19

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	346	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Interleukin-8	D, E	protein	72	Homo sapiens	P10145 (AlphaFold model)
C-X-C chemokine receptor type 2	R	protein	360	Homo sapiens	P25025
scFv16	S	protein	259	Homo sapiens

Sequence of entity 1 (A), FASTA

>6LFM_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>6LFM_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
IGRARGFSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGH
LAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVAC
GGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETG
QQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICF
FPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNC
NVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>6LFM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (D, E), FASTA

>6LFM_4 Interleukin-8 (chains D, E)
SAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQR
VVEKFLKRAENS

Sequence of entity 5 (R), FASTA

>6LFM_5 C-X-C chemokine receptor type 2 (chains R)
MEDFNMESDSFEDFWKGEDLSNYSYSSTLPPFLLDAAPCEPESLEINKYFVVIIYALVFL
LSLLGNSLVMLVILYSRVGRSVTDVYLLNLALADLLFALTLPIWAASKVNGWIFGTFLCK
VVSLLKEVNFYSGILLLACISVDRYLAIVHATRTLTQKRYLVKFICLSIWGLSLLLALPV
LLFRRTVYSSNVSPACYEDMGNNTANWRMLLRILPQSFGFIVPLLIMLFCYGFTLRTLFK
AHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTQVIQETCERRNHIDRALDATE
ILGILHSCLNPLIYAFIGQKFRHGLLKILAIHGLISKDSLPKDSRPSFVGSSSGHTSTTL

Sequence of entity 6 (S), FASTA

>6LFM_6 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structural basis of CXC chemokine receptor 2 activation and signalling. Liu, K., Wu, L., Yuan, S. et al. Nature (2020) 585:135-140. DOI 10.1038/s41586-020-2492-5 · 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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