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- PDB-8zh7: Crystal structure of N-terminal domain of N-methyl-D-aspartate re... -

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Basic information

Entry
Database: PDB / ID: 8zh7
TitleCrystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody
Components
  • Antibody #003-102 heavy chain
  • Antibody #003-102 light chain
  • Glutamate receptor ionotropic, NMDA 1
KeywordsMEMBRANE PROTEIN / Receptor / Transmembrane / Ion channel / Complex
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / Neurexins and neuroligins / ligand-gated sodium channel activity / glutamate binding / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of calcium ion transport into cytosol / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / monoatomic ion channel complex / regulation of neuronal synaptic plasticity / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / synaptic membrane / postsynaptic density membrane / brain development / visual learning / calcium ion transmembrane transport / regulation of synaptic plasticity / terminal bouton / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / dendritic spine / postsynaptic membrane / calmodulin binding / neuron projection / postsynaptic density / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm
Similarity search - Function
: / : / 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. ...: / : / 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
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNomura, N. / Kumazaki, K. / Amano, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Monoclonal humanized monovalent antibody blocking therapy for anti-NMDA receptor encephalitis.
Authors: Kanno, A. / Kito, T. / Maeda, M. / Yamaki, S. / Amano, Y. / Shimomura, T. / Anisimova, M. / Kanazawa, N. / Suzuki, K. / Razai, A. / Mihara, T. / Kubo, K. / Shimada, T. / Nakamura, K. / ...Authors: Kanno, A. / Kito, T. / Maeda, M. / Yamaki, S. / Amano, Y. / Shimomura, T. / Anisimova, M. / Kanazawa, N. / Suzuki, K. / Razai, A. / Mihara, T. / Kubo, K. / Shimada, T. / Nakamura, K. / Nomura, N. / Kondo, Y. / Okimoto, A. / Sugiyama, A. / Park, D. / Stein, I. / Petshow, S. / Vandendoren, V. / Bilic, S. / Kazimi, R. / Eastman, V. / Snipas, S.J. / Mitchell, M. / Maurer, M. / Jefson, M. / Lichter, J. / Yamajuku, D. / Shirai, H. / Adachi, M. / Hoeppner, D.J. / Kubo, S. / Zito, K. / Iizuka, T. / Flynn, P. / Matsumoto, M.
History
DepositionMay 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Antibody #003-102 heavy chain
C: Antibody #003-102 light chain
D: Glutamate receptor ionotropic, NMDA 1
E: Antibody #003-102 heavy chain
F: Antibody #003-102 light chain
G: Glutamate receptor ionotropic, NMDA 1
H: Antibody #003-102 heavy chain
I: Antibody #003-102 light chain
J: Glutamate receptor ionotropic, NMDA 1
K: Antibody #003-102 heavy chain
L: Antibody #003-102 light chain


Theoretical massNumber of molelcules
Total (without water)377,95712
Polymers377,95712
Non-polymers00
Water00
1
A: Glutamate receptor ionotropic, NMDA 1
B: Antibody #003-102 heavy chain
C: Antibody #003-102 light chain


Theoretical massNumber of molelcules
Total (without water)94,4893
Polymers94,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glutamate receptor ionotropic, NMDA 1
E: Antibody #003-102 heavy chain
F: Antibody #003-102 light chain


Theoretical massNumber of molelcules
Total (without water)94,4893
Polymers94,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Glutamate receptor ionotropic, NMDA 1
H: Antibody #003-102 heavy chain
I: Antibody #003-102 light chain


Theoretical massNumber of molelcules
Total (without water)94,4893
Polymers94,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Glutamate receptor ionotropic, NMDA 1
K: Antibody #003-102 heavy chain
L: Antibody #003-102 light chain


Theoretical massNumber of molelcules
Total (without water)94,4893
Polymers94,4893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)287.010, 287.010, 53.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 42620.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Homo sapiens (human) / References: UniProt: Q05586
#2: Antibody
Antibody #003-102 heavy chain


Mass: 26519.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Antibody #003-102 light chain


Mass: 25349.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→248.558 Å / Num. obs: 62589 / % possible obs: 100 % / Redundancy: 42.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.268 / Rrim(I) all: 0.271 / Net I/σ(I): 16.03
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.5-3.592.79447520.4822.8331
3.59-3.692.0743930.6662.0961
3.69-3.81.60344370.7841.6231
3.8-3.911.21442280.8741.231
3.91-4.040.95241350.9260.9651
4.04-4.180.72240270.9580.7321
4.18-4.340.55238110.980.5581
4.34-4.520.42137670.9870.4261
4.52-4.720.3335140.9920.3341
4.72-4.950.2834400.9940.2831
4.95-5.220.26532020.9950.2681
5.22-5.530.24530630.9950.2481
5.53-5.920.23228870.9960.2341
5.92-6.390.20526510.9950.2071
6.39-70.18224730.9960.1851
7-7.830.14522540.9980.1461
7.83-9.040.11919600.9980.121
9.04-11.070.10516420.9980.1071
11.07-15.650.09812660.9980.0991
3.5-3.592.79447520.4822.8331

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 18.15 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22724 3132 5 %RANDOM
Rwork0.18639 ---
obs0.18848 59463 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 132.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2---0.31 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24484 0 0 0 24484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01925076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.94734144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.48353184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14824.3821004
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.546154072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.64115116
X-RAY DIFFRACTIONr_chiral_restr0.1030.23868
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118792
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_it9.63213.23712784
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it15.35619.81515952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.05613.23412292
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined22.70637056
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 238 -
Rwork0.206 4505 -
obs--99.52 %

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