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- PDB-4rwa: Synchrotron structure of the human delta opioid receptor in compl... -

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Basic information

Entry
Database: PDB / ID: 4rwa
TitleSynchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (PSI community target)
Components
  • Soluble cytochrome b562,Delta-type opioid receptor
  • bifunctional peptide
KeywordsMEMBRANE PROTEIN / Human opioid receptor / bifunctional peptide / GPCR signaling / GPCR network / PSI-Biology / Structural Genomics / GPCR / membrane / Lipidic cubic phase / BRIL
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
bifunctional peptide / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsFenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. ...Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. / Wang, D. / Weierstall, U. / Spence, J.C.H. / Boutet, S. / Messerschmidt, M. / Williams, G.J. / Gati, C. / Yefanov, O.M. / White, T.A. / Oberthuer, D. / Metz, M. / Yoon, C.H. / Barty, A. / Chapman, H.N. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Fromme, P. / Tourwe, D. / Schiller, P.W. / Roth, B.L. / Ballet, S. / Katritch, V. / Stevens, R.C. / Cherezov, V. / GPCR Network (GPCR)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural basis for bifunctional peptide recognition at human delta-opioid receptor.
Authors: Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. / Wang, D. / Weierstall, U. / Spence, J.C. / Boutet, S. / ...Authors: Fenalti, G. / Zatsepin, N.A. / Betti, C. / Giguere, P. / Han, G.W. / Ishchenko, A. / Liu, W. / Guillemyn, K. / Zhang, H. / James, D. / Wang, D. / Weierstall, U. / Spence, J.C. / Boutet, S. / Messerschmidt, M. / Williams, G.J. / Gati, C. / Yefanov, O.M. / White, T.A. / Oberthuer, D. / Metz, M. / Yoon, C.H. / Barty, A. / Chapman, H.N. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Fromme, P. / Tourwe, D. / Schiller, P.W. / Roth, B.L. / Ballet, S. / Katritch, V. / Stevens, R.C. / Cherezov, V.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jun 7, 2017Group: Database references / Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562,Delta-type opioid receptor
B: Soluble cytochrome b562,Delta-type opioid receptor
G: bifunctional peptide
H: bifunctional peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9525
Polymers92,5954
Non-polymers3571
Water181
1
A: Soluble cytochrome b562,Delta-type opioid receptor
H: bifunctional peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6543
Polymers46,2982
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area19630 Å2
MethodPISA
2
B: Soluble cytochrome b562,Delta-type opioid receptor
G: bifunctional peptide


Theoretical massNumber of molelcules
Total (without water)46,2982
Polymers46,2982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.549, 86.121, 94.684
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHEAA39 - 329112 - 402
21GLYGLYPHEPHEBB39 - 329112 - 402
12ASPASPLEULEUAA1002 - 11067 - 111
22ASPASPLEULEUBB1002 - 11067 - 111

NCS ensembles :
ID
1
2
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Soluble cytochrome b562,Delta-type opioid receptor / Cytochrome b-562 / D-OR-1 / DOR-1


Mass: 45636.812 Da / Num. of mol.: 2 / Mutation: M29W, H124I, R138L,M29W, H124I, R138L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, OPRD, OPRD1, cybC / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7
#2: Protein/peptide bifunctional peptide


Type: Peptide-like / Class: Unknown / Mass: 660.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: bifunctional peptide
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 21

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 25-28% (v/v) PEG 400, 0.12 to 0.2 M NaCl, 100 mM MES buffer at pH 6.0, 1 mM DIPP-NH2 and 5% (v/v) of either one of the following additives: 30% glycerol, 1.0 M glycine or 0.01M L-glutathione ...Details: 25-28% (v/v) PEG 400, 0.12 to 0.2 M NaCl, 100 mM MES buffer at pH 6.0, 1 mM DIPP-NH2 and 5% (v/v) of either one of the following additives: 30% glycerol, 1.0 M glycine or 0.01M L-glutathione reduced/0.01M L-glutathione oxidized, Lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.28→94.61 Å / Num. obs: 18862 / % possible obs: 96.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 11.7
Reflection shellResolution: 3.3→3.51 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N6H

4n6h


Resolution: 3.28→94.61 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / SU B: 58.708 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27296 958 5.1 %RANDOM
Rwork0.23891 ---
obs0.24067 17904 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.825 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å2-0 Å2-0.31 Å2
2--1.11 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 3.28→94.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 13 1 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026067
X-RAY DIFFRACTIONr_bond_other_d0.0030.025841
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9788294
X-RAY DIFFRACTIONr_angle_other_deg0.9823.00513318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3155776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74123.622196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82415917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1211521
X-RAY DIFFRACTIONr_chiral_restr0.0560.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216769
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021348
X-RAY DIFFRACTIONr_mcbond_it3.2968.1253116
X-RAY DIFFRACTIONr_mcbond_other3.298.1243115
X-RAY DIFFRACTIONr_mcangle_it5.3612.1813888
X-RAY DIFFRACTIONr_mcangle_other5.3612.1823889
X-RAY DIFFRACTIONr_scbond_it3.2068.5892951
X-RAY DIFFRACTIONr_scbond_other3.2068.5892952
X-RAY DIFFRACTIONr_scangle_other5.34812.7474407
X-RAY DIFFRACTIONr_long_range_B_refined8.43267.9477333
X-RAY DIFFRACTIONr_long_range_B_other8.43167.957334
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A146770.12
12B146770.12
21A54740.14
22B54740.14
LS refinement shellResolution: 3.282→3.367 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 51 -
Rwork0.334 1043 -
obs--75.6 %
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)
11.53420.9663-0.45920.8739-0.00260.6679-0.00710.23170.0224-0.00570.0706-0.0410.0314-0.0332-0.06350.02140.02850.03730.11740.0440.0907-39.5996-6.640343.719
21.6549-0.97690.14520.89070.19130.4153-0.0831-0.20860.0810.05070.1275-0.1117-0.0018-0.0705-0.04440.0248-0.0039-0.04850.08530.02860.1184-38.0819-35.64133.88
33.5749-2.5950.89083.3521-1.68931.87750.12430.0462-0.17040.1549-0.01460.0881-0.13560.0702-0.10970.0698-0.02820.0070.0913-0.03230.0345-84.1413-22.935134.5952
43.43722.645-0.95352.2417-1.23462.22820.00330.10640.2309-0.09960.11160.14010.19060.0563-0.11490.06180.01070.02410.1207-0.03460.0521-81.8389-18.762412.5752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 333
2X-RAY DIFFRACTION2B39 - 330
3X-RAY DIFFRACTION3A1002 - 1106
4X-RAY DIFFRACTION4B1002 - 1106

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