[English] 日本語
Yorodumi
- PDB-6me3: XFEL crystal structure of human melatonin receptor MT1 in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6me3
TitleXFEL crystal structure of human melatonin receptor MT1 in complex with 2-phenylmelatonin
Componentschimera protein of Melatonin receptor type 1A and GlgA glycogen synthase
KeywordsMEMBRANE PROTEIN / GPCR / melatonin receptor type 1A (MT1) / 2-phenylmelatonin / XFEL / LCP / PGS / circadian rhythm / jetlag
Function / homology
Function and homology information


melatonin receptor activity / glycogen (starch) synthase activity / organic cyclic compound binding / hormone binding / Class A/1 (Rhodopsin-like receptors) / mating behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / circadian rhythm ...melatonin receptor activity / glycogen (starch) synthase activity / organic cyclic compound binding / hormone binding / Class A/1 (Rhodopsin-like receptors) / mating behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / circadian rhythm / G alpha (i) signalling events / receptor complex / G protein-coupled receptor signaling pathway / nucleotide binding / plasma membrane
Similarity search - Function
Melatonin receptor family / Melatonin receptor 1A/1B / 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 ...Melatonin receptor family / Melatonin receptor 1A/1B / 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
Chem-JEY / OLEIC ACID / DI(HYDROXYETHYL)ETHER / Melatonin receptor type 1A / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsStauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Gati, C. / Batyuk, A. / Ishchenko, A. / Brehm, W. / White, T.A. ...Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Gati, C. / Batyuk, A. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, C. / Zhu, L. / Grant, T.D. / Grandner, J.M. / Olsen, R.H.J. / Tribo, A.R. / Weierstall, U. / Roth, B.L. / Katritch, V. / Liu, W. / Cherezov, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127026 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of ligand recognition at the human MT1melatonin receptor.
Authors: Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Huang, X.P. / Gati, C. / Batyuk, A. / Slocum, S.T. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, ...Authors: Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Huang, X.P. / Gati, C. / Batyuk, A. / Slocum, S.T. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, C. / Zhu, L. / Grant, T.D. / Grandner, J.M. / Shiriaeva, A. / Olsen, R.H.J. / Tribo, A.R. / Yous, S. / Stevens, R.C. / Weierstall, U. / Katritch, V. / Roth, B.L. / Liu, W. / Cherezov, V.
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 3, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2944
Polymers56,5971
Non-polymers6973
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.400, 122.400, 122.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsAUTHORS STATE BIOLOGICAL UNIT IS UNKNOWN

-
Components

#1: Protein chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase / / Mel1a receptor / Glycogen synthase / Mel1a receptor


Mass: 56597.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Gene: MTNR1A, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P48039, UniProt: Q9V2J8
#2: Chemical ChemComp-JEY / N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide / 2-phenylmelatonin


Mass: 308.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.9→30.6 Å / Num. obs: 21336 / % possible obs: 100 % / Redundancy: 2323 % / Biso Wilson estimate: 73.87 Å2 / R split: 0.098 / Net I/σ(I): 9.4
Reflection shellResolution: 2.9→3.04 Å / Redundancy: 489.3 % / Mean I/σ(I) obs: 0.39 / R split: 2.956 / % possible all: 100
Serial crystallography measurementPulse duration: 43 fsec. / Pulse energy: 4 µJ / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Flow rate: 0.3 µL/min / Injector diameter: 50 µm / Injector nozzle: LCP / Power by: HPLC pump
Serial crystallography data reductionCrystal hits: 119563 / Frames indexed: 99897 / Frames total: 726497

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASER2.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0V

4s0v


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.929 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.462 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.455 / SU Rfree Blow DPI: 0.275 / SU Rfree Cruickshank DPI: 0.279
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1062 4.99 %RANDOM
Rwork0.203 ---
obs0.205 21300 100 %-
Displacement parametersBiso mean: 107.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.4586 Å20 Å20 Å2
2---1.4586 Å20 Å2
3---2.9173 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 49 3 3772
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093884HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985285HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1731SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes575HARMONIC5
X-RAY DIFFRACTIONt_it3884HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion3.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion513SEMIHARMONIC5
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_contact4490SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.262 135 4.84 %
Rwork0.239 2656 -
all0.24 2791 -
obs--100 %
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)
10.5733-0.33420.57530.4419-0.43246.16360.248-0.2387-0.00990.1521-0.0137-0.02180.54710.2444-0.23430.2801-0.2471-0.06320.122-0.0109-0.419221.0381-27.321936.5721
25.3913.60130.433710.69851.6324.70410.0675-0.10840.64070.195-0.0902-0.1823-0.18830.02640.0227-0.20810.0672-0.0047-0.2620.0087-0.163731.21692.42590.3557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|23 - A|318 }
2X-RAY DIFFRACTION2{ A|1001 - A|1196 }

+
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