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- PDB-4amj: Turkey beta1 adrenergic receptor with stabilising mutations and b... -

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Basic information

Entry
Database: PDB / ID: 4amj
TitleTurkey beta1 adrenergic receptor with stabilising mutations and bound biased agonist carvedilol
ComponentsBETA-1 ADRENERGIC RECEPTOR
KeywordsMEMBRANE PROTEIN / 7TMR BETA1-ADRENOCEPTOR / STABILISING MUTATIONS / BIASED AGONIST
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / regulation of circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of GTPase activity / early endosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Beta 1 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) ...Beta 1 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CVD / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWarne, T. / Edwards, P.C. / Leslie, A.G. / Tate, C.G.
CitationJournal: Structure / Year: 2012
Title: Crystal Structures of a Stabilized Beta1-Adrenoceptor Bound to the Biased Agonists Bucindolol and Carvedilol
Authors: Warne, T. / Edwards, P.C. / Leslie, A.G. / Tate, C.G.
History
DepositionMar 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Oct 31, 2012Group: Atomic model
Revision 1.3Dec 3, 2014Group: Derived calculations
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-1 ADRENERGIC RECEPTOR
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,29418
Polymers71,8822
Non-polymers5,41316
Water1,820101
1
A: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,40611
Polymers35,9411
Non-polymers3,46510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8887
Polymers35,9411
Non-polymers1,9476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.056, 62.196, 100.926
Angle α, β, γ (deg.)90.00, 109.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAAA45 - 9915 - 69
21SERSERALAALABB45 - 9915 - 69
12PHEPHELEULEUAA112 - 13282 - 102
22PHEPHELEULEUBB112 - 13282 - 102
13LEULEUVALVALAA152 - 172122 - 142
23LEULEUVALVALBB152 - 172122 - 142
14LEULEUILEILEAA175 - 177145 - 147
24LEULEUILEILEBB175 - 177145 - 147
15THRTHRLYSLYSAA203 - 235173 - 205
25THRTHRLYSLYSBB203 - 235173 - 205
16ALAALAVALVALAA288 - 312230 - 254
26ALAALAVALVALBB288 - 312230 - 254
17ASNASNALAALAAA329 - 358271 - 300
27ASNASNALAALABB329 - 358271 - 300
18VALVALARGARGAA134 - 139104 - 109
28VALVALARGARGBB134 - 139104 - 109

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999985, 0.00468, 0.003018), (0.00548, 0.730427, 0.682968), (0.000992, 0.682974, -0.730442)-14.11296, -18.35323, 46.56359

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Components

#1: Protein BETA-1 ADRENERGIC RECEPTOR / / BETA-1 ADRENORECEPTOR / BETA-1 ADRENOCEPTOR / BETA-T


Mass: 35940.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-368 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MELEAGRIS GALLOPAVO (turkey) / Cell: ERYTHROCYTE / Plasmid: PBACPAK8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P07700
#2: Chemical ChemComp-CVD / (2S)-1-(8H-CARBAZOL-4-YLOXY)-3-[2-(2-METHOXYPHENOXY)ETHYLAMINO]PROPAN-2-OL / CARVEDILOL / Carvedilol


Mass: 406.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H26N2O4 / Comment: medication*YM
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 379.489 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 90 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 90 TO VAL ENGINEERED RESIDUE IN CHAIN A, CYS 116 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 227 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 282 TO LEU ENGINEERED RESIDUE IN CHAIN A, PHE 327 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 338 TO MET ENGINEERED RESIDUE IN CHAIN A, CYS 358 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN B, MET 90 TO VAL ENGINEERED RESIDUE IN CHAIN B, CYS 116 TO LEU ENGINEERED RESIDUE IN CHAIN B, TYR 227 TO ALA ENGINEERED RESIDUE IN CHAIN B, ALA 282 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 327 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 338 TO MET ENGINEERED RESIDUE IN CHAIN B, CYS 358 TO ALA
Sequence detailsTHE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S, M90V, Y227A, A282L, F327A, F338M ...THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S, M90V, Y227A, A282L, F327A, F338M THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE EXPRESSION AND HELP CRYSTALLISATION C116L, C358A

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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: 3.71 Å3/Da / Density % sol: 66.8 % / Description: NONE
Crystal growTemperature: 277 K / pH: 9
Details: 0.1 M BICINE PH 9.0, 22% PEG 600, 4 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→52.1 Å / Num. obs: 47122 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y02

2y02


Resolution: 2.3→95.33 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.176 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24005 2378 5 %RANDOM
Rwork0.2016 ---
obs0.20354 44731 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.19 Å2
2--2.28 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→95.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 213 101 4962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024966
X-RAY DIFFRACTIONr_bond_other_d0.0010.023433
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9856718
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0098036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82522.022178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8415808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.591535
X-RAY DIFFRACTIONr_chiral_restr0.0730.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215217
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021079
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2495 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Rms dev position: 3.87 Å / Weight position: 0.5

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 174 -
Rwork0.288 3155 -
obs--98.99 %

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