7YDH: Cryo EM structure of CD97/miniG13 complex

Cryo EM structure of CD97/miniG13 complex. Determined by electron microscopy at 3.1 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,764
Mol. weight: 133.18 kDa
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

7YDH contains 32 α-helices and 58 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	9-24	16
α-helix	27-30	4
β-strand	35-39	5	1
α-helix	46-52	7
β-strand	69-76	8	1
β-strand	79-86	8	1
α-helix	95-97	3
β-strand	105-111	7	1
α-helix	115-128	14
α-helix	133-136	4
β-strand	138-144	7	1
α-helix	149-151	3
α-helix	158-160	3
α-helix	172-184	13
β-strand	195-200	6	1
α-helix	207-227	21

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
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
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	165-170	6	5
β-strand	175-181	7	5
β-strand	189-192	4	6
β-strand	198-202	5	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	241-245	5	7
β-strand	250-254	5	7
β-strand	259-264	6	7
β-strand	273-277	5	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain E: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	111	1	10
β-strand	115-119	5	10
β-strand	142-143	2	11
β-strand	147-149	3	12
β-strand	156-161	6	11
β-strand	176-180	5	12
β-strand	187-190	4	12
β-strand	204-209	6	11
β-strand	212-217	6	11
β-strand	227-231	5	12
β-strand	232	1	13
α-helix	238	1
β-strand	239	1	13
β-strand	244-247	4	12

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-44	15
α-helix	45-47	3
α-helix	56-58	3

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	545-571	27
α-helix	578-600	23
β-strand	602	1	14
α-helix	610-641	32
α-helix	652-673	22
β-strand	683	1	14
α-helix	689-691	3
α-helix	694-719	26
α-helix	722-725	4
α-helix	731-746	16
α-helix	751-758	8
α-helix	766-776	11
α-helix	778-786	9
α-helix	791-803	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G protein subunit 13 (Gi2-mini-G13 chimera)	A	protein	230	Homo sapiens	Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
scFv16	E	protein	247	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Adhesion G protein-coupled receptor E5 subunit beta	R	protein	307	Homo sapiens	P48960 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YDH_1 G protein subunit 13 (Gi2-mini-G13 chimera) (chains A)
MGSTVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 2 (B), FASTA

>7YDH_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 (E), FASTA

>7YDH_3 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 4 (G), FASTA

>7YDH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>7YDH_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 Q14344 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
9GE2 2.51 Å, Structure of GPR55 in complex with G13 and synthetic agonist ML184
7SF8 2.7 Å, GPR56 (ADGRG1) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
8ZX4 2.85 Å, LPI-bound GPR55 in complex with G13
9GE3 2.87 Å, Structure of GPR55 in complex with G13 and endogenous lipid agonist…
7SF7 2.9 Å, LPHN3 (ADGRL3) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
9E51 2.9 Å, Cryo-EM structure of human LPHN2 (ADGRL2)/G13 complex in lipid nanodiscs
9ECJ 2.9 Å, Human P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13
9IY8 3.01 Å, Cryo-EM structure of apo-GPR55-G13 complex
8ZX5 3.03 Å, AM251-bound GPR55 in complex with G13
9IZH 3.04 Å, Cryo-EM structure of LPA1-G13 complex with LPA
8KGG 3.06 Å, LPS-bound P2Y10 in complex with G13

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