[English] 日本語
Yorodumi
- PDB-4bvn: Ultra-thermostable beta1-adrenoceptor with cyanopindolol bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bvn
TitleUltra-thermostable beta1-adrenoceptor with cyanopindolol bound
ComponentsBETA-1 ADRENERGIC RECEPTOR
KeywordsSIGNALING PROTEIN
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
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-P32 / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMiller, J. / Nehme, R. / Warne, T. / Edwards, P.C. / Leslie, A.G.W. / Schertler, G. / Tate, C.G.
CitationJournal: Plos One / Year: 2014
Title: The 2.1 A Resolution Structure of Cyanopindolol-Bound Beta1- Adrenoceptor Identifies an Intramembrane Na+ Ion that Stabilises the Ligand-Free Receptor.
Authors: Miller-Gallacher, J.L. / Nehme, R. / Warne, T. / Edwards, P.C. / Schertler, G.F.X. / Leslie, A.G.W. / Tate, C.G.
History
DepositionJun 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Dec 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_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_atom_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_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,91012
Polymers35,8911
Non-polymers3,01911
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.093, 62.127, 95.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-2006-

OLC

21A-3025-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 35890.828 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 OF THE THIRD INTRACELLULAR LOOP WERE DELETED FROM THE CONSTRUCT. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 367 AND A HEXAHIS TAG ADDED.
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

-
Non-polymers , 5 types, 49 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-P32 / 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile


Mass: 287.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O2
#4: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID / ADA (buffer)


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY ...THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,I129V,Y227A,A282L,D322K,F327A, F338M,Y343L. THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE EXPRESSION AND HELP CRYSTALLISATION C116L, C358A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 25% PEG 600, 0.1M ADA PH7.0 LIPID CUBIC PHASE (LCP) TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→31.9 Å / Num. obs: 18686 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VT4

2vt4


Resolution: 2.1→30.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.814 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24552 964 5.2 %RANDOM
Rwork0.19287 ---
obs0.19558 17696 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.72 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 167 38 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022515
X-RAY DIFFRACTIONr_bond_other_d0.0020.022620
X-RAY DIFFRACTIONr_angle_refined_deg1.562.0073380
X-RAY DIFFRACTIONr_angle_other_deg0.9123.0055990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71321.74486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2891518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
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_it2.2962.871156
X-RAY DIFFRACTIONr_mcbond_other2.2952.8661155
X-RAY DIFFRACTIONr_mcangle_it3.2384.2821442
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4813.5871359
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
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 66 -
Rwork0.249 1152 -
obs--87.44 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more