6DO1: PDB entry 6DO1

Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8. Determined by X-ray diffraction at 2.9 Å resolution. Released 30 Jan 2019.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Escherichia coli, synthetic construct
Chains: 8
Atoms: 7,930
Mol. weight: 156.22 kDa
Ligands: OLC, NAG
Released: 30 Jan 2019

Explore 6DO1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DO1 contains 34 α-helices and 48 β-strands across 8 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: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	1
α-helix	25-50	26
α-helix	51-56	6
α-helix	62-89	28
α-helix	97-130	34
α-helix	133-139	7
α-helix	142-159	18
α-helix	161-166	6
β-strand	168-172	5	1
β-strand	177-181	5	1
β-strand	182-184	3	2
α-helix	193-197	5
α-helix	198-205	8
α-helix	206-230	25
α-helix	337-350	14
α-helix	353-367	15
α-helix	373-395	23
α-helix	397-402	6
α-helix	406-414	9

Chain B: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	3
α-helix	30-50	21
α-helix	51-56	6
α-helix	62-89	28
α-helix	97-130	34
α-helix	133-137	5
α-helix	142-159	18
α-helix	161-166	6
β-strand	168-172	5	3
β-strand	177-181	5	3
β-strand	182-184	3	4
α-helix	193-197	5
α-helix	198-205	8
α-helix	206-230	25
α-helix	337-367	31
α-helix	373-395	23
α-helix	397-402	6
α-helix	406-414	9

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	10-12	3	6
β-strand	17-25	9	5
β-strand	31-39	9	6
β-strand	45-52	8	6
β-strand	57-59	3	6
α-helix	61-63	3
β-strand	67-72	6	5
β-strand	77-83	7	5
α-helix	87-89	3
β-strand	91-99	9	6
β-strand	114-116	3	6
β-strand	120-124	5	6

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-13	4	8
β-strand	16-25	10	7
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-85	9	7
α-helix	87-89	3
β-strand	91-98	8	8
β-strand	114-116	3	8
β-strand	120-125	6	8

Chain E: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	9
β-strand	21-23	3	9
β-strand	34-36	3	10
β-strand	49-51	3	10
β-strand	77-79	3	9
β-strand	92-93	2	11
β-strand	95-97	3	10
β-strand	115	1	10
β-strand	120-121	2	11

Chain F: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	12
β-strand	33-37	5	13
β-strand	47-52	6	13
β-strand	57-59	3	13
α-helix	61-63	3
β-strand	67-72	6	12
β-strand	77-82	6	12
β-strand	96-97	2	13

Chains G and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein	A, B	protein	425	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P30556 (AlphaFold model)
Nanobody Nb.AT110i1	C, D, E, F	protein	126	synthetic construct
Angiotensin-like peptide S1I8	G, H	protein	8	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6DO1_1 Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein (chains A, B)
DYKDDDDKILNSSTEDGIKRIQDDCPKAGRHNYIFVMIPTLYSIIFVVGIFGNSLVVIVI
YFYMKLKTVASVFLLNLALADLCFLLTLPLWAVYTAMEYRWPFGNYLCKIASASVSFNLY
ASVFLLTCLSIDRYLAIVHPMKSRLRRTMLVAKVTCIIIWLLAGLASLPAIIHRNVFFIE
NTNITVCAFHYESQNSTLPIGLGLTKNILGFLFPFLIILTSYTLIWKALKKAYDLEDNWE
TLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDIL
VGQIDDALKLANEGKVKEAQAAAEQLKTTRNAEIQKNKPRNDDIFKIIMAIVLFFFFSWI
PHQIFTFLDVLIQLGIIRDCRIADIVDTAMPITICIAYFNNCLNPLFYGFLGKKFKRYFL
QLLKY

Sequence of entity 2 (C, D, E, F), FASTA

>6DO1_2 Nanobody Nb.AT110i1 (chains C, D, E, F)
QVQLQESGGGLVQAGGSLRLSCAASGNIFDVDIMGWYRQAPGKERELVASITDGGSTDYA
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAVAYPDIPTYFDYDSDNFYWGQGT
QVTVSS

Sequence of entity 3 (G, H), FASTA

>6DO1_3 Angiotensin-like peptide S1I8 (chains G, H)
GRVYIHPI

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Distinctive Activation Mechanism for Angiotensin Receptor Revealed by a Synthetic Nanobody. Wingler, L.M., McMahon, C., Staus, D.P. et al. Cell (2019) 176:479-490.e12. DOI 10.1016/j.cell.2018.12.006 · 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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