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- PDB-2vt4: TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND B... -

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Basic information

Entry
Database: PDB / ID: 2vt4
TitleTURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND CYANOPINDOLOL
ComponentsBETA1 ADRENERGIC RECEPTOR
KeywordsRECEPTOR / GPCR / MEMBRANE / PALMITATE / TRANSDUCER / ANTAGONIST BOUND FORM / INTEGRAL MEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTOR / G PROTEIN COUPLED RECEPTOR / THERMOSTABILISING POINT MUTATIONS / PHOSPHOPROTEIN / SEVEN-HELIX RECEPTOR / LIPOPROTEIN / 7TM RECEPTOR / GLYCOPROTEIN / TRANSMEMBRANE
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
DECANE / Chem-P32 / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWarne, A. / Serrano-Vega, M.J. / Baker, J.G. / Moukhametzianov, R. / Edwards, P.C. / Henderson, R. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X.
Citation
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Conformational Thermostabilisation of the Beta1-Adrenergic Receptor in a Detergent Resistant Form
Authors: Serrano-Vega, M.J. / Magnani, F. / Shibata, Y. / Tate, C.G.
History
DepositionMay 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA1 ADRENERGIC RECEPTOR
B: BETA1 ADRENERGIC RECEPTOR
C: BETA1 ADRENERGIC RECEPTOR
D: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,23826
Polymers143,0104
Non-polymers5,22722
Water55831
1
A: BETA1 ADRENERGIC RECEPTOR
B: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,11913
Polymers71,5052
Non-polymers2,61411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-26.9 kcal/mol
Surface area33780 Å2
MethodPQS
2
C: BETA1 ADRENERGIC RECEPTOR
D: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,11913
Polymers71,5052
Non-polymers2,61411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-38.2 kcal/mol
Surface area32900 Å2
MethodPQS
3
A: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1317
Polymers35,7531
Non-polymers1,3786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9886
Polymers35,7531
Non-polymers1,2365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1317
Polymers35,7531
Non-polymers1,3786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9886
Polymers35,7531
Non-polymers1,2365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.500, 86.800, 95.500
Angle α, β, γ (deg.)67.60, 73.30, 85.80
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 16 molecules ABCD

#1: Protein
BETA1 ADRENERGIC RECEPTOR / BETA-1 ADRENOCEPTOR / BETA-1 ADRENORECEPTOR / BETA-T


Mass: 35752.598 Da / Num. of mol.: 4 / Fragment: RESIDUES 33-243,272-276,279-367 / 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
#4: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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Non-polymers , 4 types, 41 molecules

#2: Chemical
ChemComp-P32 / 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile


Mass: 287.357 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

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 ENGINEERED RESIDUE IN CHAIN C, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN C, MET 90 TO VAL ENGINEERED RESIDUE IN CHAIN C, CYS 116 TO LEU ENGINEERED RESIDUE IN CHAIN C, TYR 227 TO ALA ENGINEERED RESIDUE IN CHAIN C, ALA 282 TO LEU ENGINEERED RESIDUE IN CHAIN C, PHE 327 TO ALA ENGINEERED RESIDUE IN CHAIN C, PHE 338 TO MET ENGINEERED RESIDUE IN CHAIN C, CYS 358 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN D, MET 90 TO VAL ENGINEERED RESIDUE IN CHAIN D, CYS 116 TO LEU ENGINEERED RESIDUE IN CHAIN D, TYR 227 TO ALA ENGINEERED RESIDUE IN CHAIN D, ALA 282 TO LEU ENGINEERED RESIDUE IN CHAIN D, PHE 327 TO ALA ENGINEERED RESIDUE IN CHAIN D, PHE 338 TO MET ENGINEERED RESIDUE IN CHAIN D, CYS 358 TO ALA
Sequence detailsRESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 AND 277-278 OF THE THIRD INTRCELLULAR LOOP ...RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 AND 277-278 OF THE THIRD INTRCELLULAR LOOP WERE DELETED FROM THE CONSTRUCT. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 367 AND A HEXAHIS TAG ADDED. 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: 2.94 Å3/Da / Density % sol: 58 %
Description: THE LYSOZYME COMPONENT OF 2RH1 WAS REMOVED FOR THE MOLECULAR REPLACEMENT
Crystal growMethod: vapor diffusion / pH: 7.1
Details: VAPOUR DIFFUSION. EQUAL VOLUMES OF PROTEIN (6MG/ML) IN 10MM TRIS-HCL PH7.7, 50MM NACL, 0.1MM EDTA, 0.35% OCTYLTHIOGLUCOSIDE, 0.5MM CYANOPINDOLOL AND RESERVOIR 0.1M ADA, PH 6.9-7.3, 29-32% PEG600.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→46.4 Å / Num. obs: 41499 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 39.32 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.PHASER)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RH1

2rh1


Resolution: 2.7→45.1 Å / SU ML: 0.44 / Phase error: 25.37 / Stereochemistry target values: ML
Details: STRICT NCS, SIGMA 0.025, APPLIED TO CHAINS A AND D AND TO CHAINS B AND C, EXCLUDING DETERGENTS
RfactorNum. reflection% reflection
Rfree0.268 2047 4.9 %
Rwork0.212 --
obs0.215 41499 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.82 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 46.32 Å2
Baniso -1Baniso -2Baniso -3
1--4.8747 Å20.4951 Å20.4051 Å2
2--8.7893 Å2-2.3976 Å2
3----3.9146 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8607 0 338 31 8976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139180
X-RAY DIFFRACTIONf_angle_d1.27212460
X-RAY DIFFRACTIONf_dihedral_angle_d26.7613384
X-RAY DIFFRACTIONf_chiral_restr0.0781451
X-RAY DIFFRACTIONf_plane_restr0.0051453

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