[English] 日本語
Yorodumi
- PDB-4gpo: Oligomeic Turkey Beta1-Adrenergic G Protein-Coupled Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gpo
TitleOligomeic Turkey Beta1-Adrenergic G Protein-Coupled Receptor
ComponentsBeta-1 adrenergic receptor
KeywordsRECEPTOR / seven-transmembrane helix receptor / G-protein coupled receptor
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 / early endosome / identical protein binding / membrane / 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
Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHuang, J.J. / Chen, S. / Zhang, J.J. / Huang, X.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Crystal structure of oligomeric beta-1-adrenergic G protein-coupled receptors in ligand-free basal state.
Authors: Huang, J. / Chen, S. / Zhang, J.J. / Huang, X.Y.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Refinement description
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-1 adrenergic receptor
B: Beta-1 adrenergic receptor


Theoretical massNumber of molelcules
Total (without water)71,5052
Polymers71,5052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-14 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.660, 79.590, 69.040
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 36:237 or resseq 280:356 )
211chain B and (resseq 36:237 or resseq 280:356 )

-
Components

#1: Protein Beta-1 adrenergic receptor / Beta-1 adrenoreceptor / Beta-1 adrenoceptor / Beta-T


Mass: 35752.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-276,279-367 / Mutation: STABILISING MUTATIONS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Gene: ADRB1 / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P07700

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20mM sodium acetate, 100-300mM ammonium sulfate, 26~30% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 291K
PH range: 3.6-4.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.35→67.57 Å / Num. obs: 17463 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 6.3
Reflection shellResolution: 3.35→3.44 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1275 / % possible all: 97

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y04

2y04


Resolution: 3.5→29.779 Å / SU ML: 1.54 / σ(F): 1.99 / Phase error: 40.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3546 642 4.94 %RANDOM
Rwork0.3099 ---
obs0.3121 13006 83.62 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.906 Å2 / ksol: 0.254 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4683 Å2-0 Å212.3701 Å2
2--3.7643 Å20 Å2
3----9.5631 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 0 0 4442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064554
X-RAY DIFFRACTIONf_angle_d1.1366205
X-RAY DIFFRACTIONf_dihedral_angle_d17.261593
X-RAY DIFFRACTIONf_chiral_restr0.084746
X-RAY DIFFRACTIONf_plane_restr0.005745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2217X-RAY DIFFRACTIONPOSITIONAL
12B2217X-RAY DIFFRACTIONPOSITIONAL0.02
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.76980.5524730.47671428X-RAY DIFFRACTION48
3.7698-4.14830.47541000.36922160X-RAY DIFFRACTION74
4.1483-4.74640.32231520.26672881X-RAY DIFFRACTION98
4.7464-5.97210.34911400.29492931X-RAY DIFFRACTION99
5.9721-29.78040.29711770.29282964X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7954-0.39590.17260.7802-0.52261.0011-0.02310.1115-0.1781-0.2534-0.13290.1042-0.03910.1053-0.07550.2712-0.06870.0922-0.2136-0.08560.3455-32.0337-0.037310.0043
21.11220.2447-0.26880.4606-0.07980.8440.3702-0.5973-0.3338-0.2171-0.04320.48350.06160.71480.7066-0.7398-0.19370.6566-0.3670.3722-0.8309-31.677914.850415.6039
30.0327-0.0144-0.06770.00520.04270.13510.0179-0.0971-0.05460.00050.0745-0.0461-0.0430.16930.06830.4548-0.1557-0.36520.9595-0.2423-0.0206-13.817229.091429.0225
40.58390.1082-0.10970.7618-0.30280.9321-0.0763-0.3164-0.1530.08640.19180.4947-0.39150.34690.01980.1652-0.0030.098-0.42420.2858-0.1209-40.846524.35726.5952
50.558-0.12840.62640.3792-0.5971.3548-0.2215-0.03020.4020.0832-0.08-0.15-0.1820.2668-0.21970.4419-0.4605-0.12320.1795-0.22580.2844-9.630226.828813.3294
63.0940.31770.8891.55310.29182.1557-0.0385-0.05830.0589-0.3286-0.03660.0436-0.1503-0.05950.09940.39270.0648-0.91640.5006-0.01960.8922-19.869118.57617.0111
72.2998-0.60091.01690.1917-0.55713.0273-0.03590.70490.2198-0.3927-0.05470.317-0.0078-0.11480.00560.71050.2702-0.80070.46270.06830.5676-33.082314.4248-5.7092
81.7356-0.52470.54741.7364-2.14762.6998-0.2679-0.5086-0.15970.1584-0.0303-0.23840.06430.4482-0.21930.29190.1552-0.10980.3679-0.3360.5314-18.16936.035719.5227
90.93660.6383-0.41170.56190.03290.9693-0.0043-0.1785-0.0662-0.2307-0.10290.0969-0.32630.20610.03350.55340.0796-0.14170.08830.03950.6228-35.32-8.45413.858
100.7269-0.09420.02530.7476-0.68751.7315-0.3173-0.19390.07860.2771-0.3312-0.42780.10360.6493-0.45150.0425-0.31620.16920.110.3032-0.1007-19.5419-22.28219.8999
111.83781.5638-0.79851.47860.15435.1686-0.00630.11490.3276-0.16710.15160.3846-0.5482-0.3470.02480.3690.072-0.3093-0.06820.16810.5556-40.9625-14.6983.192
120.9418-0.3460.14340.3565-0.07970.95090.0649-0.23480.07220.1962-0.14740.10260.05440.0496-0.2642-0.65360.45660.4497-0.2127-0.228-0.1099-31.2626-29.11513.6133
13-0.00560.002-0.0009-0.00220.00120.001-0.14710.1479-0.2235-0.24850.22910.05730.00450.1279-0.03450.68410.2191-0.3271.5539-0.27211.3272-13.2429-37.47728.4213
142.27790.11250.74431.11870.19931.2305-0.30480.06280.2196-0.360.05280.2668-0.33390.1133-0.0928-0.29090.1576-0.5946-0.00170.07670.0583-40.0747-32.8615.7378
153.08741.34790.20650.5860.09630.01510.4125-0.8612-0.38040.4597-0.268-0.31460.20610.1057-0.08550.4870.1436-0.34690.42450.0340.6947-27.7842-35.15535.823
162.0875-1.84721.42591.6583-1.36614.9132-0.1155-0.36260.19480.6684-0.0315-0.8926-0.26160.51660.12390.76420.1095-0.4950.5732-0.04020.8475-28.0644-24.73932.3494
172.2913-0.11931.23941.7004-0.03521.6306-0.05660.11590.0459-0.2312-0.15150.1726-0.1383-0.5088-0.08610.0525-0.0008-0.8840.63770.28971.0108-50.9389-28.65216.7077
180.6072-0.6399-0.36513.1116-0.09170.6221-0.007-0.06920.01060.02810.1036-0.12410.1140.07180.0480.40540.2491-0.74910.2215-0.11031.0227-36.3107-18.46920.7451
194.02733.5373-0.32298.37580.29142.574-0.111-0.1624-0.24550.13160.06520.45470.1678-0.4567-0.00791.0827-0.3367-0.07071.5914-0.20591.1822-16.1263-11.40727.9748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 35:66)A35 - 66
2X-RAY DIFFRACTION2chain 'A' and (resseq 67:140)A67 - 140
3X-RAY DIFFRACTION3chain 'A' and (resseq 141:157)A141 - 157
4X-RAY DIFFRACTION4chain 'A' and (resseq 158:217)A158 - 217
5X-RAY DIFFRACTION5chain 'A' and (resseq 218:282)A218 - 282
6X-RAY DIFFRACTION6chain 'A' and (resseq 283:315)A283 - 315
7X-RAY DIFFRACTION7chain 'A' and (resseq 316:332)A316 - 332
8X-RAY DIFFRACTION8chain 'A' and (resseq 333:356)A333 - 356
9X-RAY DIFFRACTION9chain 'B' and (resseq 35:66)B35 - 66
10X-RAY DIFFRACTION10chain 'B' and (resseq 67:92)B67 - 92
11X-RAY DIFFRACTION11chain 'B' and (resseq 93:110)B93 - 110
12X-RAY DIFFRACTION12chain 'B' and (resseq 111:140)B111 - 140
13X-RAY DIFFRACTION13chain 'B' and (resseq 141:157)B141 - 157
14X-RAY DIFFRACTION14chain 'B' and (resseq 158:217)B158 - 217
15X-RAY DIFFRACTION15chain 'B' and (resseq 218:282)B218 - 282
16X-RAY DIFFRACTION16chain 'B' and (resseq 283:302)B283 - 302
17X-RAY DIFFRACTION17chain 'B' and (resseq 303:323)B303 - 323
18X-RAY DIFFRACTION18chain 'B' and (resseq 324:345)B324 - 345
19X-RAY DIFFRACTION19chain 'B' and (resseq 346:356)B346 - 356

+
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