[English] 日本語
Yorodumi
- PDB-3nyo: Crystal Structure of G Protein-Coupled Receptor Kinase 6 in Compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nyo
TitleCrystal Structure of G Protein-Coupled Receptor Kinase 6 in Complex with AMP
ComponentsG protein-coupled receptor kinase 6
KeywordsTRANSFERASE / Kinase / GRK / RGS homology domain / G protein-coupled receptor kinase
Function / homology
Function and homology information


G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / regulation of G protein-coupled receptor signaling pathway / regulation of signal transduction / Wnt signaling pathway / G alpha (s) signalling events / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding ...G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / regulation of G protein-coupled receptor signaling pathway / regulation of signal transduction / Wnt signaling pathway / G alpha (s) signalling events / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases ...GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / (R,R)-2,3-BUTANEDIOL / G protein-coupled receptor kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.92 Å
AuthorsTesmer, J.J.G. / Singh, P.
CitationJournal: Embo J. / Year: 2010
Title: Molecular basis for activation of G protein-coupled receptor kinases.
Authors: Boguth, C.A. / Singh, P. / Huang, C.C. / Tesmer, J.J.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_ref_seq_dif.details / _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: G protein-coupled receptor kinase 6
B: G protein-coupled receptor kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,08719
Polymers131,9642
Non-polymers2,12417
Water1448
1
A: G protein-coupled receptor kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,18811
Polymers65,9821
Non-polymers1,20610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: G protein-coupled receptor kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8998
Polymers65,9821
Non-polymers9187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-187 kcal/mol
Surface area55050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.574, 154.574, 208.117
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SO4 / End label comp-ID: SO4 / Refine code: 2 / Auth seq-ID: 3 - 584 / Label seq-ID: 3

Dom-IDAuth asym-IDLabel asym-ID
1AA - J
2BB - S

-
Components

#1: Protein G protein-coupled receptor kinase 6 / G protein-coupled receptor kinase GRK6


Mass: 65981.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPRK6, GRK6 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five
References: UniProt: P43250, G-protein-coupled receptor kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 5.44 Å3/Da / Density % sol: 77.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10 mg/ml GRK6 mixed 1:1 with well containing 1.6 M AMS and 100 mM Bis-Tris, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 34428 / % possible obs: 55.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.9-2.954.30.4551.3
2.95-33.50.7023.8
3-3.063.40.4926.2
3.06-3.123.60.5269
3.12-3.193.90.43112.7
3.19-3.274.10.47116.6
3.27-3.354.20.41320.6
3.35-3.444.30.35226.9
3.44-3.544.30.35433.5
3.54-3.654.40.30442.2
3.65-3.784.50.32555.9
3.78-3.944.50.3482.9
3.94-4.114.50.289100
4.11-4.334.50.206100
4.33-4.64.50.148100
4.6-4.964.50.136100
4.96-5.454.50.115100
5.45-6.244.50.107100
6.24-7.854.50.06799.8
7.85-404.30.03999.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→30 Å / Cor.coef. Fo:Fc: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 30.305 / SU ML: 0.261 / SU R Cruickshank DPI: 0.4037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1795 -RANDOM
Rwork0.22172 ---
obs0.22172 34329 56.21 %-
all-32534 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 132.743 Å2
Baniso -1Baniso -2Baniso -3
1-5.97 Å22.98 Å20 Å2
2--5.97 Å20 Å2
3----8.95 Å2
Refinement stepCycle: LAST / Resolution: 2.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8908 0 123 8 9039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.9912450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86251102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63223.591440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.883151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9061578
X-RAY DIFFRACTIONr_chiral_restr0.0650.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216966
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.791.55518
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42628888
X-RAY DIFFRACTIONr_scbond_it0.64333704
X-RAY DIFFRACTIONr_scangle_it1.1714.53562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2208tight positional0.20.05
2293medium positional0.380.5
2208tight thermal0.170.5
2293medium thermal0.232
LS refinement shellResolution: 2.918→2.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.282 109 -
Rfree-0 -
obs--2.45 %
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)
10.0963-0.00370.13830.0320.11031.3006-0.07350.06590.0956-0.0228-0.0604-0.01540.4208-0.02150.13390.58110.00940.00490.18710.05370.115-72.66925.55320.379
20.5521.10640.69082.79131.43231.1784-0.18770.12720.0131-0.02060.163-0.139-0.15850.4680.02470.2997-0.1231-0.06270.5364-0.03340.0973-51.34350.30713.525
30.63350.3497-0.65880.2917-0.39781.4546-0.27710.14030.0291-0.06420.12020.0928-0.05960.26190.15690.4121-0.344-0.02620.58860.1420.117-56.27750.515-42.5
40.48560.14320.07953.44310.7251.006-0.15740.1381-0.1348-0.31550.12930.30760.24440.25610.02810.4991-0.02140.05250.2495-0.13640.1409-66.19419.62-34.929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 74
2X-RAY DIFFRACTION1A155 - 527
3X-RAY DIFFRACTION1A576 - 585
4X-RAY DIFFRACTION1B528 - 543
5X-RAY DIFFRACTION1C1 - 7
6X-RAY DIFFRACTION2A75 - 154
7X-RAY DIFFRACTION2B544 - 557
8X-RAY DIFFRACTION3B1 - 74
9X-RAY DIFFRACTION3B155 - 527
10X-RAY DIFFRACTION3B576 - 584
11X-RAY DIFFRACTION3A528 - 543
12X-RAY DIFFRACTION3D3 - 4
13X-RAY DIFFRACTION4B75 - 154
14X-RAY DIFFRACTION4A544 - 557

+
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