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- PDB-1y1m: Crystal structure of the NR1 ligand binding core in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1y1m
TitleCrystal structure of the NR1 ligand binding core in complex with cycloleucine
ComponentsGlutamate [NMDA] receptor subunit zeta 1
KeywordsLIGAND BINDING PROTEIN / Protein-ligand complex / ligand-binding complex
Function / homology
Function and homology information


pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration / regulation of cell communication / olfactory learning / dendritic branch / conditioned taste aversion / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity ...pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration / regulation of cell communication / olfactory learning / dendritic branch / conditioned taste aversion / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / suckling behavior / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / RAF/MAP kinase cascade / response to amine / neurotransmitter receptor complex / Synaptic adhesion-like molecules / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / ligand-gated sodium channel activity / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of synapse assembly / protein heterotetramerization / response to morphine / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / monoatomic cation transmembrane transport / positive regulation of calcium ion transport into cytosol / cellular response to glycine / associative learning / positive regulation of dendritic spine maintenance / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / monoatomic cation transport / glutamate receptor binding / social behavior / ligand-gated monoatomic ion channel activity / phosphatase binding / long-term memory / prepulse inhibition / monoatomic cation channel activity / synaptic cleft / response to fungicide / calcium ion homeostasis / cellular response to manganese ion / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor signaling pathway / sensory perception of pain / dendrite membrane / regulation of neuron apoptotic process / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / learning / sodium ion transmembrane transport / synaptic membrane / response to amphetamine / adult locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / neuron cellular homeostasis / cerebral cortex development / response to calcium ion / visual learning / regulation of synaptic plasticity / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / calcium ion transmembrane transport / calcium channel activity / memory / intracellular calcium ion homeostasis / terminal bouton / synaptic vesicle / calcium ion transport / rhythmic process / amyloid-beta binding / synaptic vesicle membrane / signaling receptor activity / protein-containing complex assembly / presynaptic membrane / dendritic spine / basolateral plasma membrane
Similarity search - Function
: / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...: / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-AMINOCYCLOPENTANECARBOXYLIC ACID / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsInanobe, A. / Gouaux, E.
CitationJournal: Neuron / Year: 2005
Title: Mechanism of Partial Agonist Action at the NR1 Subunit of NMDA Receptors.
Authors: Inanobe, A. / Furukawa, H. / Gouaux, E.
History
DepositionNov 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate [NMDA] receptor subunit zeta 1
B: Glutamate [NMDA] receptor subunit zeta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9384
Polymers66,6802
Non-polymers2582
Water12,232679
1
A: Glutamate [NMDA] receptor subunit zeta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4692
Polymers33,3401
Non-polymers1291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate [NMDA] receptor subunit zeta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4692
Polymers33,3401
Non-polymers1291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-14 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.156, 53.203, 67.546
Angle α, β, γ (deg.)110.12, 91.55, 108.69
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein Glutamate [NMDA] receptor subunit zeta 1 / nmdar nr1 / NR1 / NMD-R1 / N-methyl-D-aspartate receptor / glutamate receptor / ionotropic / N- ...nmdar nr1 / NR1 / NMD-R1 / N-methyl-D-aspartate receptor / glutamate receptor / ionotropic / N-methyl D-aspartate 1


Mass: 33340.031 Da / Num. of mol.: 2 / Fragment: ligand-binding core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: The first Gly is a cloning artifact. Two regions (residues 394:544 and 631:800) of NMZ1_RAT were connected with dipeptide of Gly and Thr
Organ: forebrain / Plasmid: pet22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): origami B / References: UniProt: P35439
#2: Chemical ChemComp-AC5 / 1-AMINOCYCLOPENTANECARBOXYLIC ACID / CYCLO-LEUCINE


Type: peptide linking / Mass: 129.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2003
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.79→46.77 Å / Num. all: 62657 / Num. obs: 59649 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 3.8
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.69 / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5772 9.7 %random
Rwork0.187 ---
all0.191 57310 --
obs0.191 57310 95.2 %-
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.1766 Å2-0.0611 Å2-0.4119 Å2
2--0.1448 Å20.3202 Å2
3---1.8725 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 18 685 4906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.00502
X-RAY DIFFRACTIONx_angle_deg1.18475

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