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- PDB-3q41: Crystal structure of the GluN1 N-terminal domain (NTD) -

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Basic information

Entry
Database: PDB / ID: 3q41
TitleCrystal structure of the GluN1 N-terminal domain (NTD)
ComponentsGlutamate [NMDA] receptor subunit zeta-1
KeywordsTRANSPORT PROTEIN / NTD / NMDA / GluN1 / ion channel / glycosylation
Function / homology
Function and homology information


pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / response to glycine / propylene metabolic process / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / glycine binding / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / response to amine / startle response / social behavior / monoatomic cation transmembrane transport / associative learning / regulation of neuronal synaptic plasticity / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / cellular response to manganese ion / glutamate receptor binding / synaptic cleft / prepulse inhibition / phosphatase binding / monoatomic cation channel activity / glutamate-gated receptor activity / calcium ion homeostasis / response to fungicide / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sensory perception of pain / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / learning / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / terminal bouton / : / visual learning / cerebral cortex development / calcium ion transmembrane transport / regulation of synaptic plasticity / calcium channel activity / memory / neuron cellular homeostasis / intracellular calcium ion homeostasis / synaptic vesicle membrane / response to calcium ion / calcium ion transport / rhythmic process / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / negative regulation of neuron apoptotic process
Similarity search - Function
: / : / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor ...: / : / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SAD,SIRAS / Resolution: 3.4 Å
AuthorsFarina, A.N. / Blain, K.Y. / Maruo, T. / Kwiatkowski, W. / Choe, S. / Nakagawa, T.
CitationJournal: J.Neurosci. / Year: 2011
Title: Separation of Domain Contacts Is Required for Heterotetrameric Assembly of Functional NMDA Receptors.
Authors: Farina, A.N. / Blain, K.Y. / Maruo, T. / Kwiatkowski, W. / Choe, S. / Nakagawa, T.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,62826
Polymers128,0263
Non-polymers3,60223
Water45025
1
A: Glutamate [NMDA] receptor subunit zeta-1
B: Glutamate [NMDA] receptor subunit zeta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,77618
Polymers85,3512
Non-polymers2,42516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-40 kcal/mol
Surface area31760 Å2
MethodPISA
2
C: Glutamate [NMDA] receptor subunit zeta-1
hetero molecules

C: Glutamate [NMDA] receptor subunit zeta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,70516
Polymers85,3512
Non-polymers2,35414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5690 Å2
ΔGint-30 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.679, 164.679, 147.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A24 - 394
2116B24 - 394
3116C24 - 394

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Components

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


Mass: 42675.469 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, UNP residues 21-393
Source method: isolated from a genetically manipulated source
Details: stably expressed in HEK cells / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: E / Gene: Grin1, Nmdar1 / Plasmid: IRES-mCherry / Cell line (production host): GnTI(-) HEK cells / Production host: Homo sapiens (human) / References: UniProt: P35439
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.5 Å3/Da / Density % sol: 72.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein in (20mM Tris-HCl pH 7.5, 150mM NaCl) was mixed 1:1 with 4M Formate and 20mM TCEP, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2010 / Details: Rigaku VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→142.6 Å / Num. all: 32023 / Num. obs: 32023 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.9
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD,SIRAS / Resolution: 3.4→45.24 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.857 / SU B: 25.524 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27929 1617 5.1 %RANDOM
Rwork0.22936 ---
obs0.23185 30371 99.8 %-
all-32023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 3.4→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8725 0 218 25 8968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.97412414
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14451106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40923.818406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.175151535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2821566
X-RAY DIFFRACTIONr_chiral_restr0.0860.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216881
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3351.55522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6328946
X-RAY DIFFRACTIONr_scbond_it0.61533619
X-RAY DIFFRACTIONr_scangle_it1.1274.53468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2887 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.685
Bloose positional0.835
Cloose positional0.765
Aloose thermal3.2110
Bloose thermal1.6810
Cloose thermal3.1410
LS refinement shellResolution: 3.403→3.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 113 -
Rwork0.292 2200 -
obs--98.72 %

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