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- PDB-6w25: Crystal structure of the Melanocortin-4 Receptor (MC4R) in comple... -

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Basic information

Entry
Database: PDB / ID: 6w25
TitleCrystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119
Components
  • Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4
  • SHU9119
KeywordsMEMBRANE PROTEIN / Melanocortin-4 Receptor / Ca++ cofactor / SHU9119 / GPCR / PGS fusion / LCP
Function / homology
Function and homology information


regulation of eating behavior / melanocyte-stimulating hormone receptor activity / response to melanocyte-stimulating hormone / melanocortin receptor activity / glycogen (starch) synthase activity / regulation of grooming behavior / energy reserve metabolic process / regulation of metabolic process / neuropeptide binding / feeding behavior ...regulation of eating behavior / melanocyte-stimulating hormone receptor activity / response to melanocyte-stimulating hormone / melanocortin receptor activity / glycogen (starch) synthase activity / regulation of grooming behavior / energy reserve metabolic process / regulation of metabolic process / neuropeptide binding / feeding behavior / insulin secretion / diet induced thermogenesis / negative regulation of feeding behavior / peptide hormone binding / positive regulation of bone resorption / Peptide ligand-binding receptors / response to insulin / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / nucleotide binding / ubiquitin protein ligase binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Melanocortin 4 receptor / Melanocortin receptor 3-5 / Melanocortin/ACTH receptor / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Melanocortin 4 receptor / Melanocortin receptor 3-5 / Melanocortin/ACTH receptor / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / 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)
Similarity search - Domain/homology
OLEIC ACID / Melanocortin receptor 4 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsYu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. ...Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. / Wu, L. / Stevens, S.N. / Peisley, A. / Williams, S.Y. / Chen, V. / Millhauser, G.L. / Zhao, S. / Cone, R.D. / Stevens, R.C.
CitationJournal: Science / Year: 2020
Title: Determination of the melanocortin-4 receptor structure identifies Ca2+as a cofactor for ligand binding.
Authors: Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. / Wu, L. / Stevens, S.N. / Peisley, A. / Williams, S.Y. / ...Authors: Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. / Wu, L. / Stevens, S.N. / Peisley, A. / Williams, S.Y. / Chen, V. / Millhauser, G.L. / Zhao, S. / Cone, R.D. / Stevens, R.C.
History
DepositionMar 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Sep 9, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Oct 18, 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 2.2Nov 15, 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: Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4
B: SHU9119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,57511
Polymers61,2762
Non-polymers2,3009
Water37821
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint6 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.910, 44.490, 88.050
Angle α, β, γ (deg.)90.000, 97.470, 90.000
Int Tables number5
Space group name H-MC121
Detailsauthors state that the biological unit is unknown

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Components

#1: Protein Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4 / MC4-R / Glycogen synthase / MC4-R


Mass: 60197.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (archaea)
Gene: MC4R, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32245, UniProt: Q9V2J8
#2: Protein/peptide SHU9119


Mass: 1078.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.9
Details: 19% PEG 400, 100 mM Bis-tris propane buffer, and 50 mM CaCl2 2H2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→43.65 Å / Num. obs: 16761 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.997 / Rmerge(I) obs: 0.234 / Net I/σ(I): 11.62
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 3.302 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 847 / CC1/2: 0.561 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3EML
Resolution: 2.75→43.65 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.878 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.027 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.916 / SU Rfree Blow DPI: 0.33 / SU Rfree Cruickshank DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.259 815 4.86 %RANDOM
Rwork0.233 ---
obs0.234 16759 100 %-
Displacement parametersBiso max: 186.18 Å2 / Biso mean: 79.91 Å2 / Biso min: 45.99 Å2
Baniso -1Baniso -2Baniso -3
1-18.0205 Å20 Å2-0.6438 Å2
2---20.4925 Å20 Å2
3---2.472 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 2.75→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 172 21 3812
Biso mean--83.98 64.26 -
Num. residues----468
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1786SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes567HARMONIC5
X-RAY DIFFRACTIONt_it3868HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion519SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4965SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3868HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5208HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion3.05
LS refinement shellResolution: 2.75→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 150 4.99 %
Rwork0.278 2854 -
all0.279 3004 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.91520.4890.32091.1073-0.24031.8296-0.07980.4999-0.0887-0.09280.0892-0.01070.10840.0938-0.0093-0.1602-0.036-0.0081-0.0653-0.0148-0.1144152.65494.8245108.6687
24.8909-0.4961-0.35462.0427-0.24232.2195-0.0389-0.3879-0.33740.16980.1061-0.04270.14670.2669-0.0672-0.2210.02660.0028-0.10280.057-0.0549181.2486-3.9922144.6664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|43 - A|320, A|2000 - A|2008 }A43 - 320
2X-RAY DIFFRACTION1{ A|43 - A|320, A|2000 - A|2008 }A2000 - 2008
3X-RAY DIFFRACTION2{ A|1001 - A|1196 }A1001 - 1196

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