8IKL: CD97-G13 complex

Cryo-EM structure of the CD97-G13 complex. Determined by electron microscopy at 2.33 Å resolution. Released 24 Jan 2024.

Method: Electron microscopy
Resolution: 2.33 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,942
Mol. weight: 102.99 kDa
Released: 24 Jan 2024

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

Secondary structure: helices and β-sheets

8IKL contains 33 α-helices and 37 β-strands across 4 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-31	24
β-strand	34-40	7	2
α-helix	46-54	9
β-strand	69-76	8	2
β-strand	79-86	8	2
α-helix	94-98	5
β-strand	105-111	7	2
α-helix	118-129	12
β-strand	138-144	7	2
α-helix	146-152	7
α-helix	158-160	3
α-helix	172-185	14
β-strand	195-199	5	2
α-helix	207-227	21

Chain B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	34-36	3
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	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
α-helix	129-131	3
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	249-254	6	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	303-308	6	9
β-strand	315-317	3	3
β-strand	320	1	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	533-536	4
α-helix	545-571	27
α-helix	573-575	3
α-helix	578-600	23
β-strand	602	1	1
α-helix	610-641	32
α-helix	652-673	22
α-helix	675-677	3
β-strand	683	1	1
α-helix	694-725	32
α-helix	732-749	18
α-helix	751-758	8
α-helix	762-764	3
α-helix	765-776	12
α-helix	778-783	6
α-helix	784-788	5
α-helix	791-800	10

Chain Y: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adhesion G protein-coupled receptor E5	R	protein	278	Homo sapiens	P48960 (AlphaFold model)
Guanine nucleotide-binding protein G(13) subunit alpha isoforms short	A	protein	229	Homo sapiens	P08754 (AlphaFold model), Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	338	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	Y	protein	71	Homo sapiens	P59768

Sequence of entity 1 (R), FASTA

>8IKL_1 Adhesion G protein-coupled receptor E5 (chains R)
SSFAILMAHYDVEDWKLTLITRVGLALSLFCLLLCILTFLLVRPIQGSRTTIHLHLCICL
FVGSTIFLAGIENEGGQVGLRCRLVAGLLHYCFLAAFCWMSLEGLELYFLVVRVFQGQGL
STRWLCLIGYGVPLLIVGVSAAIYSKGYGRPRYCWLDFEQGFLWSFLGPVTFIILCNAVI
FVTTVWKLTQKFSEINPDMKKLKKARALTITAIAQLFLLGCTWVFGLFIFDDRSLVLTYV
FTILNCLQGAFLYLLHCLLNKKVREEYRKWACLVAGGS

Sequence of entity 2 (A), FASTA

>8IKL_2 Guanine nucleotide-binding protein G(13) subunit alpha isoforms short (chains A)
GCTLSAEDKAAVERSKMIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGSG
GSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTES
LNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLVE
CFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 3 (B), FASTA

>8IKL_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (Y), FASTA

>8IKL_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains Y)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Primary citation

Conformational transitions and activation of the adhesion receptor CD97. Mao, C., Zhao, R.J., Dong, Y.J. et al. Mol Cell (2024) 84:570-583.e7. DOI 10.1016/j.molcel.2023.12.020 · 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.
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
7YDP 3.1 Å, Cryo-EM structure of CD97/miniGs 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

Browse structure collections

About this viewer

MolViewer shows 8IKL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.