6H7N: Thioredoxin 1

Activated turkey BETA1 adrenoceptor with bound partial agonist xamoterol and nanobody Nb6B9. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Oct 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Escherichia coli (strain K12), Meleagris gallopavo, Lama glama
Chains: 6
Atoms: 8,211
Mol. weight: 122.27 kDa
Ligands: 2CV, FVK
Released: 17 Oct 2018

Explore 6H7N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H7N contains 44 α-helices and 32 β-strands across 6 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.

Chains A and B: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	41-68	28
α-helix	75-89	15
α-helix	90-94	5
α-helix	95-104	10
α-helix	110-144	35
α-helix	146-152	7
α-helix	155-178	24
α-helix	187-194	8
α-helix	205-212	8
α-helix	213-217	5
α-helix	218-272	27
α-helix	283-315	33
α-helix	322-343	22
α-helix	347-356	10

Chains C and D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	10-13	4	4
β-strand	18-25	8	3
β-strand	32-39	8	4
β-strand	46-52	7	4
β-strand	57-59	3	4
α-helix	61-63	3
β-strand	67-71	5	3
β-strand	77-82	6	3
α-helix	87-89	3
β-strand	91-99	9	4
β-strand	107-110	4	4
β-strand	114-119	6	4

Chain E: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	12	1
α-helix	13-17	5
β-strand	22-28	7	1
α-helix	33-37	5
α-helix	39-48	10
β-strand	53-59	7	1
α-helix	66-69	4
β-strand	77-82	6	1
β-strand	85-91	7	1
α-helix	96-107	12

Chain F: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	2
α-helix	12	1
α-helix	13-17	5
β-strand	22-28	7	2
α-helix	33-37	5
α-helix	39-48	10
β-strand	54-59	6	2
α-helix	66-70	5
β-strand	77-82	6	2
β-strand	86-91	6	2
α-helix	96-107	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin 1	E, F	protein	109	Escherichia coli (strain K12)	P0AA25 (AlphaFold model)
Beta-1 adrenergic receptor	A, B	protein	307	Meleagris gallopavo	P07700 (AlphaFold model)
Camelid antibody fragment Nb6B9	C, D	protein	121	Lama glama

Sequence of entity 1 (E, F), FASTA

>6H7N_1 Thioredoxin 1 (chains E, F)
SDKIIHLTDDSFDTDVLKADGAILVDFWAEWSGPSKMIAPILDEIADEYQGKLTVAKLNI
DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAE

Sequence of entity 2 (A, B), FASTA

>6H7N_2 Beta-1 adrenergic receptor (chains A, B)
AAAKVMSLLMALVVLLIVAGNVLVIAAIGSTQRLQTLTNLFITSLACADLVVGLLVVPFG
ATLVVRGTWLWGSFLCELWTSLDVLCVTASIETLCVIAIDRYLAITSPFRYQSLMTRARA
KVIICTVWAISALVSFLPIMMHWWRDEDPQALKCYQDPGCCDFVTNRAYAIASSIISFYI
PLLIMIFVYLRVYREAKEQIRKIDRASKRKTSRVMAMKEHKALKTLGIIMGVFTLCWLPF
FLVNIVNVFNRDLVPDWLFVAFNWLGYANSAMNPIIYCRSPDFRKAFKRLLAFPRKADRR
LHHHHHH

Sequence of entity 3 (C, D), FASTA

>6H7N_3 Camelid antibody fragment Nb6B9 (chains C, D)
SQVQLQESGGGLVQAGGSLRLSCAASGSIFALNIMGWYRQAPGKQRELVAAIHSGGTTNY
ANSVKGRFTISRDNAANTVYLQMNSLKPEDTAVYYCNVKDFGAIIYDYDYWGQGTQVTVS
S

Ligands and cofactors

ID	Name	Formula	Copies
2CV	Hega-10	C18 H37 N O7	5
FVK	~{N}-[2-[[(2~{S})-2-oxidanyl-3-(4-oxidanylphenoxy)propyl]amino]ethyl]morpholine…	C16 H25 N3 O5	2

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

Primary citation

Molecular basis for high affinity agonist binding in GPCRs. Warne, T., Edwards, P.C., Dore, A.S. et al. bioRxiv (2018). DOI 10.1101/436212

Other PDB entries of the same protein (UniProt P0AA25 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HUA 1.1 Å, E. coli thioredoxin variant with (4R)-FluoroPro76 as single proline residue
5HR3 1.1 Å, Crystal structure of thioredoxin N106A mutant
5HR2 1.2 Å, Crystal structure of thioredoxin L94A mutant
5HR0 1.31 Å, Crystal structure of thioredoxin E101G mutant
4HU7 1.4 Å, E. coli thioredoxin variant with Pro76 as single proline residue
4HU9 1.55 Å, E. coli thioredoxin variant with (4S)-FluoroPro76 as single proline residue
4X43 1.65 Å, Structure of proline-free E. coli Thioredoxin
2TRX 1.68 Å, Crystal structure of thioredoxin from escherichia coli at 1.68 Å resolution
6Y4Y 1.75 Å, The crystal structure of human MACROD2 in space group P41212
1KEB 1.8 Å, Crystal Structure of Double Mutant M37L,P40S E.coli Thioredoxin
2EIQ 1.9 Å, Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal…
6Y4Z 1.9 Å, The crystal structure of human MACROD2 in space group P43212

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