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- PDB-6ko5: Complex structure of Ghrelin receptor with Fab -

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Basic information

Entry
Database: PDB / ID: 6ko5
TitleComplex structure of Ghrelin receptor with Fab
Components
  • Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1
  • Fab7881 Heavy Chain
  • Fab7881 Light Chain
KeywordsMEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTOR / GHRELIN / ANTAGONIST-BOUND COMPLEX
Function / homology
Function and homology information


growth hormone secretagogue receptor activity / regulation of hindgut contraction / regulation of growth hormone secretion / positive regulation of small intestinal transit / negative regulation of locomotion involved in locomotory behavior / growth hormone-releasing hormone receptor activity / regulation of gastric motility / response to follicle-stimulating hormone / regulation of transmission of nerve impulse / ghrelin secretion ...growth hormone secretagogue receptor activity / regulation of hindgut contraction / regulation of growth hormone secretion / positive regulation of small intestinal transit / negative regulation of locomotion involved in locomotory behavior / growth hormone-releasing hormone receptor activity / regulation of gastric motility / response to follicle-stimulating hormone / regulation of transmission of nerve impulse / ghrelin secretion / positive regulation of appetite / growth hormone secretion / negative regulation of norepinephrine secretion / positive regulation of small intestine smooth muscle contraction / negative regulation of macrophage apoptotic process / positive regulation of eating behavior / adult feeding behavior / negative regulation of appetite / actin polymerization or depolymerization / positive regulation of multicellular organism growth / cellular response to thyroid hormone stimulus / response to growth hormone / regulation of postsynapse organization / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of vascular endothelial cell proliferation / response to L-glutamate / negative regulation of interleukin-1 beta production / cellular response to insulin-like growth factor stimulus / response to food / positive regulation of fatty acid metabolic process / response to dexamethasone / regulation of synapse assembly / positive regulation of sprouting angiogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of interleukin-6 production / peptide hormone binding / decidualization / negative regulation of tumor necrosis factor production / postsynaptic modulation of chemical synaptic transmission / response to hormone / hormone-mediated signaling pathway / insulin-like growth factor receptor signaling pathway / Peptide ligand-binding receptors / synaptic membrane / negative regulation of insulin secretion / electron transport chain / G protein-coupled receptor activity / negative regulation of inflammatory response / Schaffer collateral - CA1 synapse / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / spermatogenesis / G alpha (q) signalling events / learning or memory / periplasmic space / electron transfer activity / neuron projection / postsynapse / G protein-coupled receptor signaling pathway / iron ion binding / membrane raft / heme binding / glutamatergic synapse / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Growth hormone secretagogue receptor/motilin receptor / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Growth hormone secretagogue receptor/motilin receptor / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-8QX / Soluble cytochrome b562 / Growth hormone secretagogue receptor type 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsShiimura, Y. / Horita, S. / Asada, H. / Hirata, K. / Iwata, S. / Kojima, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2020
Title: Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode.
Authors: Shiimura, Y. / Horita, S. / Hamamoto, A. / Asada, H. / Hirata, K. / Tanaka, M. / Mori, K. / Uemura, T. / Kobayashi, T. / Iwata, S. / Kojima, M.
History
DepositionAug 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1
H: Fab7881 Heavy Chain
L: Fab7881 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9894
Polymers95,5003
Non-polymers4891
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)253.760, 44.750, 94.400
Angle α, β, γ (deg.)90.000, 97.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1 / Cytochrome b-562 / GHS-R / GH-releasing peptide receptor / GHRP / Ghrelin receptor


Mass: 47888.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, GHSR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: Q92847
#2: Antibody Fab7881 Heavy Chain


Mass: 23331.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab7881 Light Chain


Mass: 24278.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-8QX / 6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one


Mass: 489.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26BrFN4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES (pH6.6-7.0), 400 mM potassium acetate and 36-40% polyethylene glycol (PEG) 300.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.421 Å / Num. obs: 16374 / % possible obs: 99.9 % / Redundancy: 36.167 % / Biso Wilson estimate: 74.16 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.874 / Rrim(I) all: 0.887 / Χ2: 1.218 / Net I/σ(I): 10.26 / Num. measured all: 592198 / Scaling rejects: 677
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.536.6944.3841.794780258625830.6784.44599.9
3.5-3.7337.1252.5052.8990510243624380.8552.539100.1
3.73-4.0237.3821.7574.6183699224022390.9241.781100
4.02-4.436.8841.0127.5176608207720770.9541.026100
4.4-4.936.3280.611.8168878189918960.9820.60999.8
4.9-5.6233.3930.47713.3557636172517260.9830.484100.1
5.62-6.832.8550.4313.647442144414440.9870.436100
6.8-9.2737.9450.24327.5244661117811770.9960.24699.9
9.27-49.42135.2440.1941.7279848007940.9970.19399.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0V

4s0v


Resolution: 3.3→49.421 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2576 849 5.19 %
Rwork0.2105 --
obs0.2131 16355 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 266.37 Å2 / Biso mean: 81.4096 Å2 / Biso min: 32.25 Å2
Refinement stepCycle: final / Resolution: 3.3→49.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 31 0 6543
Biso mean--66.63 --
Num. residues----835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026700
X-RAY DIFFRACTIONf_angle_d0.5059114
X-RAY DIFFRACTIONf_chiral_restr0.0391048
X-RAY DIFFRACTIONf_plane_restr0.0041134
X-RAY DIFFRACTIONf_dihedral_angle_d14.7523996
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.3001-3.50680.31221260.27792572
3.5068-3.77740.34931350.24762561
3.7774-4.15740.27941420.21612539
4.1574-4.75860.24721540.18942552
4.7586-5.99360.24121410.1872596
5.9936-49.4210.21411510.20042686
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)
15.19135.0661.56266.7341-0.5193.3902-0.45251.0440.4563-0.15750.56460.44280.09290.5595-0.24290.7798-0.12550.17271.2009-0.17061.318440.068-47.66-19.471
22.68492.092-1.61671.8559-1.35645.01451.0225-2.18042.5410.598-0.39960.3964-1.51181.3281-0.93592.29390.62860.80951.7204-0.19751.236139.283-29.14-9.845
33.098-3.19960.54174.75331.73473.7333-0.26031.1226-2.654-0.9748-0.5370.82880.23460.14990.38881.77280.484-0.47771.5222-0.39772.129645.05-23.262-7.693
42.13530.8410.06721.8149-3.27977.60310.24721.1483-1.65540.7268-0.2134-0.55551.67680.58890.01520.896-0.0466-0.0851.3257-0.51491.514149.692-43.468-12.386
52.29980.53731.53432.05560.59781.15590.6061-1.4208-0.15620.427-0.2747-0.1591-0.34580.4295-0.41271.0443-0.25460.22951.4460.04710.822742.645-49.928-8.979
60.8523-0.33540.65124.3982-0.51972.1512-0.1762-0.1592-0.3321-0.01020.35180.2840.3029-0.1417-0.14670.3683-0.0031-0.09350.67510.11070.3626-3.342-23.1859.96
72.0572-1.1022.14957.78280.21082.50310.9829-0.2823-1.1977-1.3345-1.529-0.55110.73341.00290.42460.78930.42210.0081.64490.33281.2566-28.181-11.30721.819
83.0494-0.85730.76833.1315-0.9093.71820.25750.08570.2581-0.17260.11020.53160.0343-0.5655-0.04830.38060.1349-0.04080.77320.32160.4491-12.017-9.89911.623
98.6223-0.5564-1.49962.4003-0.63910.48420.3809-0.2382-0.4978-0.497-0.1021-0.38620.15580.1043-0.29380.54440.10630.06190.7024-0.01110.423320.395-13.3327.138
105.77566.0008-5.77377.4219-4.55627.05030.7911-1.69880.05010.6846-0.6866-0.0115-0.43770.8284-0.06350.51640.1704-0.05320.67560.13660.3009-0.777-13.63225.126
118.0520.43684.46192.46821.15023.4235-1.38811.19341.01020.1239-0.2334-0.44380.0611.63111.57660.99140.21520.10820.75220.34891.0416-31.323-29.88638.074
124.1496-0.7056-1.11752.7431-0.1583.8091-0.157-0.1957-0.71920.14920.058-0.22760.36210.1283-0.00640.60980.1515-0.03630.71760.28160.3205-6.6-24.3823.812
138.15794.9647-0.08417.40471.16814.3294-0.5735-0.46250.2921-0.03190.6157-0.2194-0.3358-0.1735-0.07550.49540.0884-0.0070.57420.0930.60782.111-28.91617.684
146.66980.4251-4.25112.10361.13043.652-0.4847-0.4822-0.2199-0.1852-0.18570.33591.17990.4060.67870.91170.1321-0.08420.87210.31890.777-21.449-35.9258.04
154.0523-0.8534-2.15975.347-0.37283.58840.07840.46030.0545-0.7397-0.2686-0.2127-0.3036-0.33780.14820.86980.07320.00630.53220.07120.3295-45.49-21.23346.652
160.69750.1319-0.70920.38510.53591.72030.04190.2614-0.3097-0.4157-0.17550.4663-0.5717-0.4046-0.01120.62560.129-0.17380.49220.16920.6776-56.007-14.18860.577
172.9194-2.78342.77316.2427-1.68866.9091-0.3991-0.24620.51960.8922-0.34210.4136-0.3765-0.07790.09170.4775-0.05980.05120.4713-0.04490.5161-60.544-13.24185.152
181.8235-0.17631.71015.9348-0.01268.40620.01250.12730.471-0.161-0.3687-0.0215-0.34010.4560.31430.32480.08410.02730.35390.02750.6076-56.236-11.01275.805
195.3590.2638-2.35453.6383-0.24528.1848-0.34050.1124-0.3414-0.6518-0.1648-0.36470.31590.46080.45410.77040.10940.06690.33850.06160.6033-40.107-41.25157.92
202.5708-1.3265-3.00021.86782.76974.6939-0.13330.04720.0178-0.1958-0.11720.43790.2059-0.08240.19180.4872-0.0087-0.00310.24720.02870.6251-53.853-28.18971.515
213.7857-4.6426-1.08926.21870.56334.84290.4592-0.1805-1.1593-0.5445-0.63950.80640.1785-0.07260.15470.4534-0.1437-0.01080.5989-0.01870.7969-65.039-27.64279.446
224.769-4.52170.09084.6954-1.51226.738-0.5857-0.7986-0.17690.48840.32870.8806-0.3193-1.2830.10450.3727-0.03980.02990.7136-0.10610.8979-71.326-20.3786.194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1002:1042 )A1002 - 1042
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1043:1048 )A1043 - 1048
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1049:1055 )A1049 - 1055
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1056:1081 )A1056 - 1081
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1082:1106 )A1082 - 1106
6X-RAY DIFFRACTION6( CHAIN A AND RESID 39:146 )A39 - 146
7X-RAY DIFFRACTION7( CHAIN A AND RESID 147:156 )A147 - 156
8X-RAY DIFFRACTION8( CHAIN A AND RESID 157:174 )A157 - 174
9X-RAY DIFFRACTION9( CHAIN A AND RESID 175:200 )A175 - 200
10X-RAY DIFFRACTION10( CHAIN A AND RESID 201:239 )A201 - 239
11X-RAY DIFFRACTION11( CHAIN A AND RESID 240:253 )A240 - 253
12X-RAY DIFFRACTION12( CHAIN A AND RESID 254:289 )A254 - 289
13X-RAY DIFFRACTION13( CHAIN A AND RESID 290:326 )A290 - 326
14X-RAY DIFFRACTION14( CHAIN A AND RESID 327:339 )A327 - 339
15X-RAY DIFFRACTION15( CHAIN H AND RESID 1:105 )H1 - 105
16X-RAY DIFFRACTION16( CHAIN H AND RESID 106:129 )H106 - 129
17X-RAY DIFFRACTION17( CHAIN H AND RESID 130:150 )H130 - 150
18X-RAY DIFFRACTION18( CHAIN H AND RESID 151:218 )H151 - 218
19X-RAY DIFFRACTION19( CHAIN L AND RESID 1:81 )L1 - 81
20X-RAY DIFFRACTION20( CHAIN L AND RESID 82:144 )L82 - 144
21X-RAY DIFFRACTION21( CHAIN L AND RESID 145:177 )L145 - 177
22X-RAY DIFFRACTION22( CHAIN L AND RESID 178:219 )L178 - 219

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