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- PDB-4rwd: XFEL structure of the human delta opioid receptor in complex with... -

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Basic information

Entry
Database: PDB / ID: 4rwd
TitleXFEL structure of the human delta opioid receptor in complex with a bifunctional peptide
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 / X-ray free-electron laser / serial femtosecond crystallography / BRIL
Function / homology
Function and homology information


electron transfer activity / periplasmic space / 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 / OLEIC ACID / (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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.7 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 2, 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 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 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_related_exp_data_set / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_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 1.5Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Dec 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)95,68816
Polymers92,5954
Non-polymers3,09312
Water48627
1
A: Soluble cytochrome b562,Delta-type opioid receptor
H: bifunctional peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8818
Polymers46,2982
Non-polymers1,5836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-9 kcal/mol
Surface area20490 Å2
MethodPISA
2
B: Soluble cytochrome b562,Delta-type opioid receptor
G: bifunctional peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8078
Polymers46,2982
Non-polymers1,5096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-13 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.230, 89.290, 96.420
Angle α, β, γ (deg.)90.00, 92.30, 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
11GLYGLYGLNGLNAA39 - 331112 - 404
21GLYGLYGLNGLNBB39 - 331112 - 404
12ALAALALEULEUAA1001 - 11066 - 111
22ALAALALEULEUBB1001 - 11066 - 111

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

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABGH

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


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

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Non-polymers , 4 types, 39 molecules

#3: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 36083

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 0.1M MES pH 6.0, 10-180mM Lithium citrate, 30-32% (v/v) PEG400, Lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.6 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Feb 2, 2014
RadiationMonochromator: K-B Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.7→33.5 Å / Num. obs: 36838 / % possible obs: 100 % / Redundancy: 560 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 209 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N6H, PDB entry 4EIY

4n6h

4eiy


Resolution: 2.7→33.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 25.109 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23803 1831 5 %RANDOM
Rwork0.20827 ---
obs0.20973 34699 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.361 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20.2 Å2
2---0.41 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6163 0 136 27 6326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026425
X-RAY DIFFRACTIONr_bond_other_d0.0030.026316
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.9948723
X-RAY DIFFRACTIONr_angle_other_deg0.8483.00514458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3825799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90923.991213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.357151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0681522
X-RAY DIFFRACTIONr_chiral_restr0.0480.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217057
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021397
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_it1.9395.3093202
X-RAY DIFFRACTIONr_mcbond_other1.9395.3093201
X-RAY DIFFRACTIONr_mcangle_it3.1527.9623999
X-RAY DIFFRACTIONr_mcangle_other3.1527.9624000
X-RAY DIFFRACTIONr_scbond_it2.1025.6293223
X-RAY DIFFRACTIONr_scbond_other2.1025.633224
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5018.3054725
X-RAY DIFFRACTIONr_long_range_B_refined5.07443.1067264
X-RAY DIFFRACTIONr_long_range_B_other5.07443.1097265
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 / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16560
12B16560
21A6178
22B6178
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 122 -
Rwork0.313 2533 -
obs--99.96 %
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)
11.91341.15710.09511.47880.00690.0852-0.05760.15160.0393-0.06130.10410.08020.00470.0235-0.04640.0122-0.02640.0070.0754-0.02380.1372-44.2788-5.178944.3416
22.1211-1.37330.0111.4971-0.03740.0493-0.0523-0.1823-0.03040.02460.11790.104-0.0094-0.0024-0.06560.0090.01960.01450.0577-0.00310.1699-42.534925.25673.8623
34.4524-2.7198-1.042.93411.54310.96810.0268-0.06990.05290.08990.04550.02660.11250.0156-0.07230.1042-0.0257-0.01450.09870.01680.1295-0.991512.576935.2715
44.01672.28070.70742.62450.89710.7710.09930.0323-0.1152-0.14660.0848-0.0279-0.2007-0.0562-0.18410.08250.01610.0390.10680.02070.08611.15297.36312.9432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 333
2X-RAY DIFFRACTION2B39 - 332
3X-RAY DIFFRACTION3A1001 - 1106
4X-RAY DIFFRACTION4B1001 - 1106

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