[English] 日本語
Yorodumi
- PDB-5tin: Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tin
TitleCrystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607
ComponentsGlycine receptor subunit alpha-3
KeywordsTRANSPORT PROTEIN / LIGAND-GATED ION CHANNEL NEUROTRANSMITTER RECEPTOR MEMBRANE PROTEIN CYS-LOOP RECEPTOR
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / glycine binding / presynaptic modulation of chemical synaptic transmission / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity ...glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / glycine binding / presynaptic modulation of chemical synaptic transmission / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity / presynaptic membrane / perikaryon / postsynaptic membrane / intracellular membrane-bounded organelle / dendrite / metal ion binding / plasma membrane
Similarity search - Function
Glycine receptor alpha3 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region ...Glycine receptor alpha3 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-7C6 / GLYCINE / Glycine receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsShaffer, P.L. / Huang, X. / Chen, H.
CitationJournal: To Be Published
Title: Crystal Structures of Human GlyRa3 Bound to a Novel Class of Potentiators with Efficacy in a Mouse Model of Neuropathic Pain
Authors: Huang, X. / Shaffer, P.L. / Ayube, S. / Bregman, H. / Chen, H. / Lehto, S.G. / Luther, J.A. / Matson, D.J. / McDonough, S.I. / Michelsen, K. / Plant, M.M. / Schneider, S. / Simard, J.R. / ...Authors: Huang, X. / Shaffer, P.L. / Ayube, S. / Bregman, H. / Chen, H. / Lehto, S.G. / Luther, J.A. / Matson, D.J. / McDonough, S.I. / Michelsen, K. / Plant, M.M. / Schneider, S. / Simard, J.R. / Teffera, Y. / Yi, S. / Zhang, M. / DiMauro, E.F. / Gingras, J.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycine receptor subunit alpha-3
B: Glycine receptor subunit alpha-3
C: Glycine receptor subunit alpha-3
D: Glycine receptor subunit alpha-3
E: Glycine receptor subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,10221
Polymers209,3575
Non-polymers2,74516
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25290 Å2
ΔGint-310 kcal/mol
Surface area64710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.301, 136.787, 192.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA8 - 3448 - 344
21METMETILEILEBB8 - 3448 - 344
12METMETTYRTYRAA8 - 3458 - 345
22METMETTYRTYRCC8 - 3458 - 345
13METMETILEILEAA8 - 3448 - 344
23METMETILEILEDD8 - 3448 - 344
14METMETTYRTYRAA8 - 3458 - 345
24METMETTYRTYREE8 - 3458 - 345
15METMETILEILEBB8 - 3448 - 344
25METMETILEILECC8 - 3448 - 344
16ALAALALYSLYSBB6 - 3466 - 346
26ALAALALYSLYSDD6 - 3466 - 346
17METMETILEILEBB8 - 3448 - 344
27METMETILEILEEE8 - 3448 - 344
18METMETILEILECC8 - 3448 - 344
28METMETILEILEDD8 - 3448 - 344
19METMETTYRTYRCC8 - 3458 - 345
29METMETTYRTYREE8 - 3458 - 345
110METMETILEILEDD8 - 3448 - 344
210METMETILEILEEE8 - 3448 - 344

NCS ensembles :
ID
10
1
2
3
4
5
6
7
8
9

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Glycine receptor subunit alpha-3


Mass: 41871.426 Da / Num. of mol.: 5 / Fragment: UNP residues 34-460, with 343-418 deleted / Mutation: N38Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75311

-
Non-polymers , 5 types, 416 molecules

#2: Chemical
ChemComp-7C6 / (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one


Mass: 401.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H19N3O5S
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.53 Å3/Da / Density % sol: 72.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 105901 / % possible obs: 98.4 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.42
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.749 / % possible all: 86.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-20002.3.8data collection
HKL-20002.3.8data scaling
PDB_EXTRACT3.2data extraction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIF

3rif


Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.475 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2006 1.9 %RANDOM
Rwork0.204 ---
obs0.205 105901 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.86 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å20 Å20 Å2
2--6.32 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13562 0 171 400 14133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214109
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213198
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.96619239
X-RAY DIFFRACTIONr_angle_other_deg0.793.00130131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13623.581606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.496152264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191572
X-RAY DIFFRACTIONr_chiral_restr0.0610.22165
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115718
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023331
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_it1.8634.0536810
X-RAY DIFFRACTIONr_mcbond_other1.8624.0526806
X-RAY DIFFRACTIONr_mcangle_it2.9916.0768495
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A205550.04
12B205550.04
21A207040.03
22C207040.03
31A206580.03
32D206580.03
41A206760.03
42E206760.03
51B205980.04
52C205980.04
61B207490.03
62D207490.03
71B205590.03
72E205590.03
81C206440.03
82D206440.03
91C207110.03
92E207110.03
101D206130.02
102E206130.02
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 132 -
Rwork0.307 6679 -
obs--84.6 %
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)
10.2670.05350.1360.63090.57420.60440.0347-0.1641-0.00170.0443-0.10060.03310.0393-0.20240.06590.1927-0.02610.00320.216-0.07270.0475-55.607-24.82229.59
20.36690.12460.15060.47690.59810.89960.01740.0230.1158-0.0499-0.05750.0605-0.1235-0.11620.04010.21020.05210.00810.0789-0.01950.066-44.071-9.29913.613
30.2382-0.0103-0.08530.30980.52070.99310.0619-0.02250.0457-0.06150.0286-0.0722-0.1470.0027-0.09050.22090.01120.01290.094-0.06660.0615-19.187-12.14416.622
40.26060.0003-0.05960.63710.6980.83250.0624-0.1332-0.01120.04440.0772-0.12080.05080.1157-0.13960.21480.0505-0.05270.1493-0.05510.0559-15.365-29.80134.136
50.36710.01820.07380.90420.74040.72130.0539-0.2836-0.06540.1409-0.0284-0.03340.1846-0.0672-0.02550.2686-0.0212-0.02140.22170.04970.015-37.979-37.80242.191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 401
2X-RAY DIFFRACTION2B6 - 401
3X-RAY DIFFRACTION3C8 - 401
4X-RAY DIFFRACTION4D5 - 401
5X-RAY DIFFRACTION5E8 - 401

+
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