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- PDB-8hdk: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with g... -

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Basic information

Entry
Database: PDB / ID: 8hdk
TitleStructure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (minor class in symmetry)
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2C
KeywordsMEMBRANE PROTEIN / NMDA receptor / GluN2C
Function / homology
Function and homology information


directional locomotion / 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 ...directional locomotion / 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 / suckling behavior / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport / RAF/MAP kinase cascade / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / response to morphine / regulation of axonogenesis / neuromuscular process controlling balance / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / response to amine / parallel fiber to Purkinje cell synapse / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / positive regulation of calcium ion transport into cytosol / cellular response to glycine / associative learning / excitatory synapse / positive regulation of dendritic spine maintenance / monoatomic cation transport / social behavior / regulation of neuronal synaptic plasticity / glutamate receptor binding / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / long-term memory / synaptic cleft / prepulse inhibition / phosphatase binding / positive regulation of synaptic transmission, glutamatergic / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / regulation of neuron apoptotic process / cellular response to manganese ion / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / synaptic membrane / response to amphetamine / 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 / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / response to calcium ion / postsynaptic density membrane / neuron cellular homeostasis / cerebral cortex development / negative regulation of protein catabolic process / visual learning / regulation of synaptic plasticity / calcium ion transmembrane transport / response to wounding / calcium channel activity / memory / long-term synaptic potentiation / intracellular calcium ion homeostasis / terminal bouton / synaptic vesicle / synaptic vesicle membrane / calcium ion transport / rhythmic process / signaling receptor activity
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 / Glutamate receptor ionotropic, NMDA 2C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 4.3 Å
AuthorsZhang, M. / Zhang, J. / Guo, F. / Li, Y. / Zhu, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
Citation
Journal: Nat Struct Mol Biol / Year: 2023
Title: Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits.
Authors: Jilin Zhang / Ming Zhang / Qinrui Wang / Han Wen / Zheyi Liu / Fangjun Wang / Yuhang Wang / Fenyong Yao / Nan Song / Zengwei Kou / Yang Li / Fei Guo / Shujia Zhu /
Abstract: N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di- ...N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di-heterotetramer (di-receptor), rat N1-N2C di-receptor and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a best resolution of 3.0 Å. The bilobate N-terminal domain (NTD) in N2D intrinsically adopts a closed conformation, leading to a compact NTD tetramer in the N1-N2D receptor. Additionally, crosslinking the ligand-binding domain (LBD) of two N1 protomers significantly elevated the channel open probability (Po) in N1-N2D di-receptors. Surprisingly, the N1-N2C di-receptor adopted both symmetric (minor) and asymmetric (major) conformations, the latter further locked by an allosteric potentiator, PYD-106, binding to a pocket between the NTD and LBD in only one N2C protomer. Finally, the N2A and N2C subunits in the N1-N2A-N2C tri-receptor display a conformation close to one protomer in the N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse function in major NMDA receptor subtypes.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits
Authors: Zhang, M. / Zhu, S.
History
DepositionNov 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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: Glutamate receptor ionotropic, NMDA 2C
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,49324
Polymers354,9574
Non-polymers6,53620
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 89724.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Homo sapiens (human) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2C / GluN2C / Glutamate [NMDA] receptor subunit epsilon-3 / N-methyl D-aspartate receptor subtype 2C / ...GluN2C / Glutamate [NMDA] receptor subunit epsilon-3 / N-methyl D-aspartate receptor subtype 2C / NMDAR2C / NR2C


Mass: 87753.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2c / Production host: Homo sapiens (human) / References: UniProt: Q00961
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#5: 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.: 12
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
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160DIRECT ELECTRON DE-10 (5k x 4k)
2160DIRECT ELECTRON DE-10 (5k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1cryoSPARCparticle selection1
4GctfCTF correction1
10cryoSPARCinitial Euler assignment1
11cryoSPARCfinal Euler assignment1
12cryoSPARCclassification1
13cryoSPARC3D reconstruction1
14cryoSPARCparticle selection2
15GctfCTF correction2
16cryoSPARCinitial Euler assignment2
17cryoSPARC3.1final Euler assignment2
18cryoSPARCclassification2
19cryoSPARC3D reconstruction2
20RELION3.13D reconstruction2
Image processing
IDImage recording-ID
11
22
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
21PHASE FLIPPING AND AMPLITUDE CORRECTION
32PHASE FLIPPING AND AMPLITUDE CORRECTION
42PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
IDImage processing-IDNum. of particles selected
111188229
21
321188229
42
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
14.3FSC 0.143 CUT-OFF1547918HDKPOINT
24.3FSC 0.143 CUT-OFF1547918HDKPOINT
34.3FSC 0.143 CUT-OFF1547928HDKPOINT
44.3FSC 0.143 CUT-OFF1547928HDKPOINT

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