8YFS: MRGPRE-Gq-scFv16-complex

MRGPRE-Gq-scFv16-complex. Determined by electron microscopy at 2.8 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Rattus norvegicus, Bos taurus, synthetic construct
Chains: 5
Atoms: 7,783
Mol. weight: 152.35 kDa
Ligands: A1D6H
Released: 5 Mar 2025

Explore 8YFS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YFS contains 32 α-helices and 59 β-strands across 5 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	33-40	8	1
α-helix	47-55	9
β-strand	182-189	8	1
β-strand	192-199	8	1
α-helix	210-213	4
β-strand	218-224	7	1
α-helix	231-242	12
β-strand	251-257	7	1
α-helix	260-266	7
α-helix	273-275	3
α-helix	278-282	5
α-helix	299-316	18
β-strand	319	1	2
β-strand	322	1	2
β-strand	324-328	5	1
α-helix	336-355	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	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
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-307	4	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	53-55	3

Chain R: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	55-76	22
α-helix	85-112	28
α-helix	120-151	32
α-helix	153-154	2
α-helix	155-159	5
α-helix	164-168	5
α-helix	172-184	13
α-helix	185-189	5
α-helix	195-223	29
α-helix	238-243	6
α-helix	245-261	17
α-helix	272-285	14
α-helix	287-293	7

Chain S: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
β-strand	128-129	2	12
β-strand	134-136	3	13
β-strand	143-149	7	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
β-strand	191-196	6	12
β-strand	199-204	6	12
β-strand	213-219	7	13
α-helix	225-226	2
β-strand	231-234	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gq protein alpha subunit	A	protein	359	Rattus norvegicus	P21279 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	344	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	70	Bos taurus	P63212 (AlphaFold model)
scFv16	S	protein	267	synthetic construct
Mrgpre	R	protein	330	Equus quagga	A0A9L0JPP9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YFS_1 Gq protein alpha subunit (chains A)
CTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNGYS
EEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAE
LAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTS
GIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKS
IWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVT
RAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNLV

Sequence of entity 2 (B), FASTA

>8YFS_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8YFS_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 4 (S), FASTA

>8YFS_4 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELLEENLYFQGASHHHHHHHH

Sequence of entity 5 (R), FASTA

>8YFS_5 MRGPRE (chains R)
AHEPRNDSMGVSPRPQPWPSHPNNGSELPTAANATAHATSVDGAHAFSAYENTLFLATVL
VSLCGLVGNGTVIWLLGFRIKRNPFSVYILNLAGADFAFLFCKSVRFLLLVLNRSVAVLN
VLIRGVTFSSYLGGLSLLMAVSVERCLSVLFPIWYRCRRLAQLSAIACALIWGLSLCMGI
LVFLCVHFVDFLCDVVNLVYNGMFFLTFLVLCASSLALLIWVQCFSMRRQPARLSRIVLL
TVLAFLVLGLPLGAGLLADRLSPSLPCFDILLPILHLLSALNSGVNPLIYFFMGRQRQQR
GQKPLREVLQSALTEDVELIREEPPSPDDT

Ligands and cofactors

ID	Name	Formula	Copies
A1D6H	(~{E})-3-(2-methoxyphenyl)prop-2-enal	C10 H10 O2	1

Primary citation

MRGPRE-Gq-scFv16-complex. Zhong, Y.N. To be published.

Other PDB entries of the same protein (UniProt P21279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5DO9 2.6 Å, Structure of regulator of G protein signaling 8 (RGS8) in complex with AlF4-activated…
7SQ2 2.6 Å, Reprocessed and refined structure of Phospholipase C-beta and Gq signaling complex
4EKD 2.71 Å, Structure of human regulator of G protein signaling 2 (RGS2) in complex with murine…
3AH8 2.9 Å, Structure of heterotrimeric G protein Galpha-q beta gamma in complex with an inhibitor…
4QJ3 3.0 Å, Structure of a fragment of human phospholipase C-beta3 delta472-559, in complex with…
2BCJ 3.06 Å, Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and…
4QJ4 3.3 Å, Structure of a fragment of human phospholipase C-beta3 delta472-569, bound to IP3 and in…
4QJ5 3.41 Å, Structure of a fragment of human phospholipase C-beta3 delta472-581, bound to IP3 and in…
2RGN 3.5 Å, Crystal Structure of p63RhoGEF complex with Galpha-q and RhoA
4GNK 4.0 Å, Crystal structure of Galphaq in complex with full-length human PLCbeta3
4EKC 7.4 Å, Structure of human regulator of G protein signaling 2 (RGS2) in complex with murine…

Browse structure collections

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