7YDM: CD97/Gq complex

Cryo-EM structure of CD97/Gq complex. Determined by electron microscopy at 2.89 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 2.89 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,131
Mol. weight: 139.56 kDa
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

7YDM contains 30 α-helices and 47 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	16-37	22
β-strand	40-46	7	1
α-helix	53-59	7
β-strand	207-214	8	1
β-strand	217-224	8	1
α-helix	234-238	5
β-strand	243-249	7	1
α-helix	266-277	12
β-strand	287-292	6	1
α-helix	294-303	10
α-helix	308-310	3
α-helix	313-317	5
α-helix	326-327	2
α-helix	332-349	18
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	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	88-94	7	3
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	189-192	4	6
β-strand	198-202	5	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	249-254	6	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 G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-21	15
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-84	7	9
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-126	5	10

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	533-536	4
α-helix	545-571	27
α-helix	578-600	23
β-strand	602	1	11
α-helix	610-641	32
α-helix	652-673	22
β-strand	683	1	11
α-helix	689-691	3
α-helix	694-719	26
α-helix	722-725	4
α-helix	734-746	13
α-helix	752-758	7
α-helix	766-775	10
α-helix	778-786	9
α-helix	791-803	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
engineered mini-Gaq	A	protein	362	Homo sapiens	P63092 (AlphaFold model), 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	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Nb35	N	protein	161	Lama glama
Adhesion G protein-coupled receptor E5 subunit beta	R	protein	307	Homo sapiens	P48960

Sequence of entity 1 (A), FASTA

>7YDM_1 engineered mini-Gaq (chains A)
MMGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVN
GYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFM
TAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRV
KTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALND
FKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDP
RVTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYN
LV

Sequence of entity 2 (B), FASTA

>7YDM_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>7YDM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>7YDM_4 Nb35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSAAALEHHHHHH

Sequence of entity 5 (R), FASTA

>7YDM_5 Adhesion G protein-coupled receptor E5 subunit beta (chains R)
MSSFAILMAHYDVEDWKLTLITRVGLALSLFCLLLCILTFLLVRPIQGSRTTIHLHLCIC
LFVGSTIFLAGIENEGGQVGLRCRLVAGLLHYCFLAAFCWMSLEGLELYFLVVRVFQGQG
LSTRWLCLIGYGVPLLIVGVSAAIYSKGYGRPRYCWLDFEQGFLWSFLGPVTFIILCNAV
IFVTTVWKLTQKFSEINPDMKKLKKARALTITAIAQLFLLGCTWVFGLFIFDDRSLVLTY
VFTILNCLQGAFLYLLHCLLNKKVREEYRKWACLVAGGSKYSEFTSTTSGTGHNQTRALR
ASESGIL

Primary citation

Structural basis of CD97 activation and G-protein coupling. Wang, N., Qian, Y., Xia, R. et al. Cell Chem Biol (2023) 30:1343-1353.e5. DOI 10.1016/j.chembiol.2023.08.003 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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