6B73: PDB entry 6B73

Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor. Determined by X-ray diffraction at 3.1 Å resolution. Released 17 Jan 2018.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Escherichia coli, Homo sapiens, Lama glama
Chains: 4
Atoms: 6,142
Mol. weight: 126.05 kDa
Ligands: CVV, CLR, OLA
Released: 17 Jan 2018

Explore 6B73 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B73 contains 30 α-helices and 26 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: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	55-56	2
α-helix	58-83	26
α-helix	84-88	5
α-helix	93-108	16
α-helix	109-111	3
α-helix	112-121	10
α-helix	127-161	35
α-helix	163-167	5
α-helix	172-196	25
β-strand	197-200	4	1
β-strand	209-212	4	1
α-helix	222-231	10
α-helix	232-236	5
α-helix	237-254	18
α-helix	263-299	37
α-helix	306-326	21
α-helix	327-331	5
α-helix	335-338	4

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-83	26
α-helix	84-88	5
α-helix	93-121	29
α-helix	127-161	35
α-helix	163-167	5
α-helix	172-196	25
β-strand	197-200	4	2
β-strand	209-212	4	2
α-helix	222-230	9
α-helix	231-236	6
α-helix	237-255	19
α-helix	263-299	37
α-helix	306-326	21
α-helix	327-331	5
α-helix	332-333	2

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	3
β-strand	12-14	3	4
β-strand	20-25	6	3
β-strand	32-39	8	4
β-strand	45-51	7	4
β-strand	58-60	3	4
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-99	8	4
β-strand	113	1	4
β-strand	118-122	5	4

Chain D: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	5
β-strand	12-14	3	6
β-strand	20-25	6	5
β-strand	32-39	8	6
β-strand	45-51	7	6
β-strand	58-60	3	6
β-strand	68-73	6	5
β-strand	78-83	6	5
β-strand	92-99	8	6
β-strand	113	1	6
β-strand	118-122	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562, kappa-type opioid receptor	A, B	protein	418	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P41145 (AlphaFold model)
Nanobody	C, D	protein	134	Lama glama

Sequence of entity 1 (A, B), FASTA

>6B73_1 Soluble cytochrome b562, kappa-type opioid receptor (chains A, B)
GGTTMADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDS
PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGSISPAIPV
IITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTTMPFQSTVYL
MNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINI
CIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVL
IIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPIHIFILVEALG
STSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTS

Sequence of entity 2 (C, D), FASTA

>6B73_2 Nanobody (chains C, D)
MAQVQLVESGGGLVRPGGSLRLSCVDSERTSYPMGWFRRAPGKEREFVASITWSGIDPTY
ADSVADRFTTSRDVANNTLYLQMNSLKHEDTAVYYCAARAPVGQSSSPYDYDYWGQGTQV
TVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
CVV	N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorph…	C27 H27 I N2 O3	2
CLR	Cholesterol	C27 H46 O	2
OLA	Oleic acid	C18 H34 O2	1

Primary citation

Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor. Che, T., Majumdar, S., Zaidi, S.A. et al. Cell (2018) 172:55-67.e15. DOI 10.1016/j.cell.2017.12.011 · 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

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