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- PDB-6h7n: ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST XA... -

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Basic information

Entry
Database: PDB / ID: 6h7n
TitleACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST XAMOTEROL AND NANOBODY Nb6B9
Components
  • Beta-1 adrenergic receptor
  • Camelid antibody fragment Nb6B9
  • Thioredoxin 1
KeywordsIMMUNE SYSTEM / Beta1 Adrenoceptor / Activated / Partial Agonist / Nanobody
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / regulation of circadian sleep/wake cycle, sleep / DNA polymerase processivity factor activity / protein-disulfide reductase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / cell redox homeostasis / positive regulation of GTPase activity / early endosome / membrane ...beta1-adrenergic receptor activity / positive regulation of heart contraction / regulation of circadian sleep/wake cycle, sleep / DNA polymerase processivity factor activity / protein-disulfide reductase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / cell redox homeostasis / positive regulation of GTPase activity / early endosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta 1 adrenoceptor / Thioredoxin / Adrenoceptor family / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Serpentine type 7TM GPCR chemoreceptor Srsx / Glutaredoxin ...Beta 1 adrenoceptor / Thioredoxin / Adrenoceptor family / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Serpentine type 7TM GPCR chemoreceptor Srsx / Glutaredoxin / Glutaredoxin / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FVK / Beta-1 adrenergic receptor / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Meleagris gallopavo (turkey)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWarne, T. / Edwards, P.C. / Dore, A.S. / Leslie, A.G.W. / Tate, C.G.
CitationJournal: Biorxiv / Year: 2018
Title: Molecular basis for high affinity agonist binding in GPCRs
Authors: Warne, T. / Edwards, P.C. / Dore, A.S. / Leslie, A.G.W. / Tate, C.G.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Thioredoxin 1
A: Beta-1 adrenergic receptor
F: Thioredoxin 1
B: Beta-1 adrenergic receptor
C: Camelid antibody fragment Nb6B9
D: Camelid antibody fragment Nb6B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,26915
Polymers119,6476
Non-polymers2,6229
Water45025
1
E: Thioredoxin 1
A: Beta-1 adrenergic receptor
C: Camelid antibody fragment Nb6B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3248
Polymers59,8243
Non-polymers1,5015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Thioredoxin 1
B: Beta-1 adrenergic receptor
D: Camelid antibody fragment Nb6B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9457
Polymers59,8243
Non-polymers1,1214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.410, 121.533, 130.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21F
12A
22B
13C
23D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUEA3 - 1073 - 107
21LYSLYSLEULEUFC3 - 1073 - 107
12ALAALAALAALAAB40 - 3582 - 292
22ALAALAALAALABD40 - 3582 - 292
13GLNGLNSERSERCE1 - 1192 - 120
23GLNGLNSERSERDF1 - 1192 - 120

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 4 molecules EFAB

#1: Protein Thioredoxin 1 / / Trx-1


Mass: 11784.370 Da / Num. of mol.: 2 / Mutation: C32S,C35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: trxA, fipA, tsnC, b3781, JW5856 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0AA25
#2: Protein Beta-1 adrenergic receptor / / Beta-1 adrenoreceptor / Beta-T


Mass: 35002.777 Da / Num. of mol.: 2 / Mutation: R68S,M90V,C116L,F327A,F338M,C358A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Gene: ADRB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07700

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Antibody , 1 types, 2 molecules CD

#3: Antibody Camelid antibody fragment Nb6B9


Mass: 13036.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 34 molecules

#4: Chemical ChemComp-FVK / ~{N}-[2-[[(2~{S})-2-oxidanyl-3-(4-oxidanylphenoxy)propyl]amino]ethyl]morpholine-4-carboxamide


Mass: 339.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N3O5
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes-NaOH pH7.5 and 21-24% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→41.5 Å / Num. obs: 64594 / % possible obs: 100 % / Redundancy: 11.9 % / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.56 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0174refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P0G, 2H6X

3p0g

2h6x


Resolution: 2.5→41.5 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.875 / SU B: 12.367 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 1.769 / ESU R Free: 0.401 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26631 1821 5 %RANDOM
Rwork0.24762 ---
obs0.24862 34374 56.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20 Å2
2--0.31 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.5→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 170 25 8211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198359
X-RAY DIFFRACTIONr_bond_other_d0.0010.028039
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.96711344
X-RAY DIFFRACTIONr_angle_other_deg0.8672.99218546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84851024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47423.303327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.904151364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571546
X-RAY DIFFRACTIONr_chiral_restr0.0590.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021750
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4346.1074117
X-RAY DIFFRACTIONr_mcbond_other2.4346.1074116
X-RAY DIFFRACTIONr_mcangle_it4.1999.1515134
X-RAY DIFFRACTIONr_mcangle_other4.1999.1515135
X-RAY DIFFRACTIONr_scbond_it2.0326.2724242
X-RAY DIFFRACTIONr_scbond_other2.0326.2724242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6139.3186211
X-RAY DIFFRACTIONr_long_range_B_refined6.18969.4629060
X-RAY DIFFRACTIONr_long_range_B_other6.18969.4679061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E55960.1
12F55960.1
21A195980.04
22B195980.04
31C77000.02
32D77000.02
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 13 -
Rwork0.418 522 -
obs--11.4 %

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