8IKJ: Inactive CD97

Cryo-EM structure of the inactive CD97. Determined by electron microscopy at 3.2 Å resolution. Released 14 Feb 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 1
Atoms: 4,200
Mol. weight: 73.22 kDa
Ligands: NAG
Released: 14 Feb 2024

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

Secondary structure: helices and β-sheets

8IKJ contains 18 α-helices and 17 β-strands across 1 chain. 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 R: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	259-264	6
α-helix	266-267	2
α-helix	273-288	16
α-helix	294-310	17
α-helix	320-342	23
β-strand	348-353	6	1
β-strand	359-365	7	1
β-strand	371-374	4	2
β-strand	379-384	6	2
α-helix	386-389	4
β-strand	397-403	7	1
α-helix	407-409	3
β-strand	416	1	3
α-helix	420-430	11
β-strand	436-438	3	3
β-strand	441	1	3
β-strand	445-450	6	1
β-strand	462-467	6	2
α-helix	479-487	9
β-strand	491-501	11	3
β-strand	505-509	5	3
β-strand	513-519	7	2
β-strand	522-527	6	2
β-strand	532-541	10	3
α-helix	549-571	23
α-helix	578-600	23
β-strand	602	1	4
α-helix	610-642	33
α-helix	652-673	22
β-strand	683	1	4
α-helix	692-718	27
α-helix	735-755	21
α-helix	767-782	16
α-helix	783-788	6
α-helix	791-800	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Adhesion G protein-coupled receptor…	R	protein	655	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P48960 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>8IKJ_1 Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Adhesion G protein-coupled receptor E5 subunit beta (chains R)
EDMTFSTWTPPPGVHSQTLSRFFDKVQDLGRDSKTSSAEVTIQNVIKLVDELMEAPGDVE
ALAPPVRHLIATQLLSNLEDIMRILAKSLPKGPFTYISPSNTELTLMIQERGDKNVTMGQ
SSARMKLNWAVAAGAEDPGPAVAGILSIQNMTTLLANASLNLHSKKQAELEEIYESSIRG
VQLRRLSAVNSIFLSHNNTKELNSPILFAFSHLESSDGEAGRDPPAKDVMPGPRQELLCA
FWKSDSDRGGHWATEGCQVLGSKNGSTTCQCSSLSSFAILMAHYDVEDWKLTLITRVGLA
LSLFCLLLCILTFLLVRPIQGSRTTIHLHLCICLFVGSTIFLAGIENEGGQVGLRCRLVA
GLLHYCFLAAFCWMSLEGLELYFLVVRVFQGQGLSTRWLCLIGYGVPLLIVGVSAAIYSK
GYGRPRYCWLDFEQGFLWSFLGPVTFIILCNAVIFVTTVWKLTQLAADLEDNWETLNDNL
KVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDD
ALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLQKARALTITAIAQLFLLGCTW
VFGLFIFDDRSLVLTYVFTILNCLQGAFLYLLHCLLNKKVREEYRKWACLVAGGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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 P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

Browse structure collections

About this viewer

MolViewer shows 8IKJ 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.