7YDP: CD97/miniGs complex

Cryo-EM structure of CD97/miniGs complex. Determined by electron microscopy at 3.1 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,028
Mol. weight: 139.58 kDa
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

7YDP contains 34 α-helices and 49 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	14-39	26
β-strand	41-47	7	2
α-helix	53-61	9
β-strand	208-214	7	2
β-strand	217-223	7	2
α-helix	236-238	3
β-strand	243-249	7	2
α-helix	266-277	12
β-strand	286-292	7	2
α-helix	294-303	10
α-helix	308-310	3
α-helix	313-317	5
α-helix	332-351	20
β-strand	359-360	2	2
β-strand	363	1	2
α-helix	371-390	20

Chain B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	5
β-strand	58-60	3	6
β-strand	63	1	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	120-125	6	7
β-strand	135-140	6	7
β-strand	146-153	8	8
β-strand	156-161	6	8
β-strand	166-170	5	8
β-strand	175-180	6	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	208-212	5	9
β-strand	218-222	5	9
β-strand	229-232	4	10
β-strand	241-245	5	10
β-strand	249-254	6	10
α-helix	255-257	3
β-strand	259-264	6	10
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	303-308	6	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-41	12
α-helix	45-47	3

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	10-12	3	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	46-51	6	4
β-strand	58-59	2	4
α-helix	62-64	3
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-98	7	4
β-strand	118	1	4
β-strand	122-126	5	4

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	533-536	4
α-helix	545-571	27
α-helix	578-600	23
α-helix	608-609	2
α-helix	610-641	32
α-helix	652-668	17
β-strand	678	1	1
β-strand	686	1	1
α-helix	689-694	6
α-helix	698-725	28
α-helix	731-748	18
α-helix	752-757	6
α-helix	765-774	10
α-helix	778-783	6
α-helix	784-788	5
α-helix	791-801	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adhesion G protein-coupled receptor E5 subunit beta	R	protein	307	Homo sapiens	P48960 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
engineered miniGas	A	protein	361	Homo sapiens	P63092 (AlphaFold model), P63096 (AlphaFold model)
Nb35	D	protein	161	Lama glama
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873

Sequence of entity 1 (R), FASTA

>7YDP_1 Adhesion G protein-coupled receptor E5 subunit beta (chains R)
MSSFAILMAHYDVEDWKLTLITRVGLALSLFCLLLCILTFLLVRPIQGSRTTIHLHLCIC
LFVGSTIFLAGIENEGGQVGLRCRLVAGLLHYCFLAAFCWMSLEGLELYFLVVRVFQGQG
LSTRWLCLIGYGVPLLIVGVSAAIYSKGYGRPRYCWLDFEQGFLWSFLGPVTFIILCNAV
IFVTTVWKLTQKFSEINPDMKKLKKARALTITAIAQLFLLGCTWVFGLFIFDDRSLVLTY
VFTILNCLQGAFLYLLHCLLNKKVREEYRKWACLVAGGSKYSEFTSTTSGTGHNQTRALR
ASESGIL

Sequence of entity 2 (C), FASTA

>7YDP_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (A), FASTA

>7YDP_3 engineered miniGas (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L

Sequence of entity 4 (D), FASTA

>7YDP_4 Nb35 (chains D)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSAAALEHHHHHH

Sequence of entity 5 (B), FASTA

>7YDP_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

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 P48960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BOU 1.9 Å, EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with barium.
8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
7YDM 2.89 Å, Cryo-EM structure of CD97/Gq complex
7YDJ 3.03 Å, Cryo EM structure of CD97/miniG12 complex
7YDH 3.1 Å, Cryo EM structure of CD97/miniG13 complex
9MQR 3.16 Å, A8 Fab in complex with CD97
7DO4 3.2 Å, Crystal structure of CD97-CD55 complex
8IKJ 3.2 Å, Cryo-EM structure of the inactive CD97

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