[English] 日本語
Yorodumi
- PDB-4n6h: 1.8 A Structure of the human delta opioid 7TM receptor (PSI Commu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n6h
Title1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
ComponentsSoluble cytochrome b562, Delta-type opioid receptor chimeric protein
KeywordsSIGNALING PROTEIN / human opioid receptor / sodium regulation / allostery / functional selectivity / GPCR signaling / constitutive activity / GPCR network / membrane protein / PSI-Biology / Structural Genomics / GPCR / membrane
Function / homology
Function and homology information


G protein-coupled enkephalin receptor activity / positive regulation of CREB transcription factor activity / spine apparatus / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / cellular response to toxic substance / receptor serine/threonine kinase binding / neuropeptide binding / eating behavior / neuronal dense core vesicle ...G protein-coupled enkephalin receptor activity / positive regulation of CREB transcription factor activity / spine apparatus / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / cellular response to toxic substance / receptor serine/threonine kinase binding / neuropeptide binding / eating behavior / neuronal dense core vesicle / regulation of calcium ion transport / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / negative regulation of protein-containing complex assembly / axon terminus / dendrite membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / adult locomotory behavior / regulation of mitochondrial membrane potential / response to nicotine / electron transport chain / postsynaptic density membrane / cellular response to growth factor stimulus / synaptic vesicle membrane / positive regulation of peptidyl-serine phosphorylation / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / G alpha (i) signalling events / Interleukin-4 and Interleukin-13 signaling / periplasmic space / electron transfer activity / neuron projection / immune response / iron ion binding / G protein-coupled receptor signaling pathway / negative regulation of gene expression / heme binding / plasma membrane
Similarity search - Function
Delta opioid receptor / Cytochrome c/b562 / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serpentine type 7TM GPCR chemoreceptor Srsx ...Delta opioid receptor / Cytochrome c/b562 / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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
Chem-EJ4 / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Soluble cytochrome b562 / Delta-type opioid receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFenalti, G. / Giguere, P.M. / Katritch, V. / Huang, X.-P. / Thompson, A.A. / Han, G.W. / Cherezov, V. / Roth, B.L. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2014
Title: Molecular control of delta-opioid receptor signalling.
Authors: Fenalti, G. / Giguere, P.M. / Katritch, V. / Huang, X.P. / Thompson, A.A. / Cherezov, V. / Roth, B.L. / Stevens, R.C.
History
DepositionOct 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references / Structure summary
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Soluble cytochrome b562, Delta-type opioid receptor chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08824
Polymers45,8781
Non-polymers6,21023
Water1,820101
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.230, 72.851, 84.408
Angle α, β, γ (deg.)90.00, 107.48, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Soluble cytochrome b562, Delta-type opioid receptor chimeric protein / D-OR-1 / DOR-1


Mass: 45878.055 Da / Num. of mol.: 1
Fragment: UNP P0ABE7 residues 23-128, UNP P41143 residues 36-338
Mutation: M1007W, H1102I, R1106L, P37S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: OPRD, OPRD1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: P41143

-
Non-polymers , 7 types, 124 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-EJ4 / (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol / Naltrindole


Mass: 414.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N2O3 / Comment: antagonist*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 47

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 293 K / Method: lcp
Details: 31-34% (v/v) PEG 400, 0.095 to 0.12 M K/Na tartrate, 5% (v/v) ethylene glycol, 100 mM MES buffer at pH 6.1-6.2, LCP, temperature 293K
PH range: 6.1-6.2

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDApr 20, 2013mirrors
MARMOSAIC 300 mm CCD2CCDJun 16, 2013mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 45488 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EJ4

4ej4


Resolution: 1.8→29.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.568 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFINEMENT REMARKS: THERE ARE SOME UNKNOWN DENSITIES LOCATED NEAR THE LIGAND BINDING SITE. THEY HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19028 2303 5.1 %RANDOM
Rwork0.17175 ---
obs0.17271 43157 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.313 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20.03 Å2
2---0.41 Å2-0 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 341 101 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023541
X-RAY DIFFRACTIONr_bond_other_d0.0010.023611
X-RAY DIFFRACTIONr_angle_refined_deg1.4192.0454750
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0038321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8525422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63622.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7471516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 171 -
Rwork0.247 3042 -
obs--95.85 %
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)
10.34440.04770.07410.65880.20690.6698-0.0226-0.0115-0.0199-0.048-0.07210.04740.0507-0.01060.09480.0339-0.01740.0060.0364-0.00170.0962-8.9959-76.804381.263
20.9849-0.2111.01880.3599-0.49992.7845-0.0743-0.0170.0353-0.0051-0.05710.1218-0.2915-0.0250.13140.0584-0.0058-0.0370.0813-0.00750.1265-16.3698-65.793278.0154
32.08840.48643.75090.28690.18859.7128-0.0116-0.1624-0.06350.0277-0.0737-0.0645-0.2435-0.07950.08520.0381-0.0254-0.02040.06750.01580.1328-0.9442-58.914387.3015
41.00020.2074-0.39950.701-0.22421.816-0.045-0.0429-0.0551-0.0622-0.0825-0.22780.0940.09290.12750.0203-0.00690.01170.05320.01320.1491.4619-70.997280.8764
54.79184.6555-2.95045.4607-2.19332.6758-0.07660.0649-0.19370.09310.018-0.19660.0090.06030.05860.1111-0.0131-0.00390.14290.00980.1624-7.0092-85.0311100.4162
614.984910.25344.651911.6274-2.77839.16880.2291-0.95260.46140.6306-0.35680.3183-0.6032-0.60320.12780.1905-0.14010.06350.4798-0.14890.05125.8891-79.171944.4659
75.71375.83153.44067.17982.71215.27410.4666-0.74020.29420.5084-0.3440.3522-0.2418-0.5618-0.12250.1424-0.07410.04830.2543-0.03760.11490.7476-83.823234.9878
88.67270.6953-2.17222.61160.07084.13410.0401-0.76870.27540.6093-0.0244-0.00480.35020.4335-0.01570.2732-0.1523-0.06150.48290.04070.20322.5178-76.464443.1862
96.44933.01121.91312.1627-0.76594.64450.1975-0.1137-0.12690.0371-0.01040.02590.08220.0082-0.18710.0315-0.0399-0.01680.07220.02290.11924.9625-88.256828.2689
105.79362.77115.80425.04244.04414.04370.6657-0.7299-0.3790.7156-0.64750.12611.1596-0.0004-0.01820.1417-0.0962-0.01580.28120.08330.11412.4431-88.396840.4387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 153
2X-RAY DIFFRACTION2A154 - 207
3X-RAY DIFFRACTION3A208 - 248
4X-RAY DIFFRACTION4A249 - 319
5X-RAY DIFFRACTION5A320 - 338
6X-RAY DIFFRACTION6A1002 - 1012
7X-RAY DIFFRACTION7A1013 - 1043
8X-RAY DIFFRACTION8A1044 - 1063
9X-RAY DIFFRACTION9A1064 - 1089
10X-RAY DIFFRACTION10A1090 - 1106

+
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