[English] 日本語
Yorodumi
- PDB-6h7l: ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST DO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h7l
TitleACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST DOBUTAMINE 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 rate by epinephrine-norepinephrine / regulation of circadian sleep/wake cycle, sleep / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / DNA polymerase processivity factor activity / protein-disulfide reductase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / cell redox homeostasis / early endosome / identical protein binding ...beta1-adrenergic receptor activity / positive regulation of heart rate by epinephrine-norepinephrine / regulation of circadian sleep/wake cycle, sleep / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / DNA polymerase processivity factor activity / protein-disulfide reductase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / cell redox homeostasis / early endosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
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
DOBUTAMINE / 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: 2.7 Å
AuthorsWarne, T. / Edwards, P.C. / Dore, A.S. / Leslie, A.G.W. / Tate, C.G.
CitationJournal: Science / Year: 2019
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 / Structure summary
Category: audit_author / pdbx_struct_assembly ...audit_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _audit_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,71119
Polymers119,6476
Non-polymers4,06413
Water25214
1
E: Thioredoxin 1
A: Beta-1 adrenergic receptor
C: Camelid antibody fragment Nb6B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,42511
Polymers59,8243
Non-polymers2,6018
Water362
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)61,2868
Polymers59,8243
Non-polymers1,4635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.513, 119.699, 129.156
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: _ / Refine code: _

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
21LYSLYSLEULEUFD3 - 1073 - 107
12ALAALAALAALAAB40 - 3582 - 292
22ALAALAALAALABE40 - 3582 - 292
13GLNGLNSERSERCC1 - 1202 - 121
23GLNGLNSERSERDF1 - 1202 - 121

NCS ensembles :
ID
1
2
3

-
Components

-
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

-
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) / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 27 molecules

#4: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-Y00 / DOBUTAMINE


Mass: 301.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23NO3 / Comment: medication*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes-NaOH pH7.5 and 21-24% PEG1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.7→41.08 Å / Num. obs: 50091 / % possible obs: 99.4 % / Redundancy: 15.8 % / Net I/σ(I): 4.9
Reflection shellResolution: 2.7→2.79 Å

-
Processing

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

2h6x

3p0g


Resolution: 2.7→41.08 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.779 / SU B: 18.284 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.496 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27826 1416 4.8 %RANDOM
Rwork0.24088 ---
obs0.24267 28040 58.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å20 Å2
2--0.42 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.7→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8014 0 252 14 8280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028435
X-RAY DIFFRACTIONr_bond_other_d0.0010.028124
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.98111435
X-RAY DIFFRACTIONr_angle_other_deg0.888318756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02351023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82323.467323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.303151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741546
X-RAY DIFFRACTIONr_chiral_restr0.0610.21334
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021748
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_it3.1036.3474113
X-RAY DIFFRACTIONr_mcbond_other3.1026.3464112
X-RAY DIFFRACTIONr_mcangle_it5.2619.5095129
X-RAY DIFFRACTIONr_mcangle_other5.269.515130
X-RAY DIFFRACTIONr_scbond_it2.6756.5164322
X-RAY DIFFRACTIONr_scbond_other2.6756.5164322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7399.6776307
X-RAY DIFFRACTIONr_long_range_B_refined7.74872.1649197
X-RAY DIFFRACTIONr_long_range_B_other7.74872.179198
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)
11E56760.09
12F56760.09
21A196160.04
22B196160.04
31C74200.02
32D74200.02
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 19 -
Rwork0.452 441 -
obs--12.61 %

+
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://pdbjlvh1.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