7YDJ: Cryo EM structure of CD97/miniG12 complex

Cryo EM structure of CD97/miniG12 complex. Determined by electron microscopy at 3.03 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,751
Mol. weight: 146.57 kDa
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

7YDJ contains 34 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-37	22
β-strand	41-46	6	1
α-helix	50-64	15
β-strand	210-213	4	1
β-strand	218-221	4	1
α-helix	231-234	4
α-helix	235-237	3
β-strand	243-249	7	1
α-helix	256-267	12
α-helix	270-272	3
β-strand	276-282	7	1
α-helix	284-292	9
α-helix	310-312	3
α-helix	313-322	10
β-strand	332-333	2	1
β-strand	336	1	1
α-helix	341-363	23

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-52	6	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	146-153	8	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	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	260-264	5	7
β-strand	273-278	6	8
β-strand	285-289	5	8
β-strand	294-297	4	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain E: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-12	3	10
β-strand	15-24	10	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
α-helix	53-55	3
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-86	9	9
β-strand	92-99	8	10
β-strand	111	1	10
β-strand	115-119	5	10
β-strand	129-130	2	11
β-strand	134-136	3	12
β-strand	143-148	6	11
β-strand	162-167	6	12
β-strand	174-178	5	12
β-strand	182-183	2	12
α-helix	184	1
β-strand	191-196	6	11
β-strand	199-204	6	11
β-strand	214-219	6	12
α-helix	225	1
β-strand	231-234	4	12

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-22	16
α-helix	30-43	14
α-helix	56-58	3

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	533-536	4
α-helix	545-571	27
α-helix	578-599	22
α-helix	610-641	32
α-helix	652-673	22
α-helix	675-677	3
β-strand	678	1	13
β-strand	686	1	13
α-helix	689-691	3
α-helix	694-725	32
α-helix	731-748	18
α-helix	755-758	4
α-helix	765-775	11
α-helix	778-783	6
α-helix	784-788	5
α-helix	791-803	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
engineered mini-G12	A	protein	345	Homo sapiens	P63096 (AlphaFold model), Q03113 (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

Sequence of entity 1 (A), FASTA

>7YDJ_1 engineered mini-G12 (chains A)
MMGCTLSAEDKAAVERSKMIDALLARERRAVRRLVKILLLGADNSGKSTFLKQMRIIHVN
GYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFM
TAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRV
KTKGIVEHDFVIKKIPFKMVDVGAQRSQRQKWFQCFDGITSILFMVDSSDYNRLVESMND
FETIVNNKLFFNVSIILFLNKMDLLVEKVKTVSIKKHFPDFRGDPHRLEDVQRYLVQCFD
RKRRNRSKPLFHHFTTSIDTENARFIFHAVKDTILQENLKDIMLQ

Sequence of entity 2 (B), FASTA

>7YDJ_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

>7YDJ_3 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 4 (G), FASTA

>7YDJ_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>7YDJ_5 Adhesion G protein-coupled receptor E5 subunit beta (chains R)
MSSFAILMAHYDVEDWKLTLITRVGLALSLFCLLLCILTFLLVRPIQGSRTTIHLHLCIC
LFVGSTIFLAGIENEGGQVGLRCRLVAGLLHYCFLAAFCWMSLEGLELYFLVVRVFQGQG
LSTRWLCLIGYGVPLLIVGVSAAIYSKGYGRPRYCWLDFEQGFLWSFLGPVTFIILCNAV
IFVTTVWKLTQKFSEINPDMKKLKKARALTITAIAQLFLLGCTWVFGLFIFDDRSLVLTY
VFTILNCLQGAFLYLLHCLLNKKVREEYRKWACLVAGGSKYSEFTSTTSGTGHNQTRALR
ASESGIL

Primary citation

Cryo EM structure of CD97/miniG12 complex. He, Y., Wang, N. To be published.

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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