[English] 日本語
Yorodumi
- EMDB-8581: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8581
TitleTriheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, Ro 25-6981, MK-801 and a GluN2B-specific Fab, at pH 6.5
Map dataoriginal map
Samplemembrane protein
  • (N-methyl-D-aspartate receptor subunit ...) x 2
  • Ionotropic glutamate receptor subunit NR2B
  • GluN2B-specific Fab, termed 11D1
  • ligand
Function/homologyN-methyl D-aspartate receptor 2B3 C-terminus / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to magnesium ion / Ionotropic glutamate receptor, metazoa ...N-methyl D-aspartate receptor 2B3 C-terminus / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to magnesium ion / Ionotropic glutamate receptor, metazoa / extracellularly glutamate-gated ion channel activity / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligand-gated ion channel / Ionotropic glutamate receptor / Receptor, ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / Receptor family ligand binding region / protein heterotetramerization / Periplasmic binding protein-like I / postsynaptic membrane / response to zinc ion / cell junction / intracellular / integral component of plasma membrane / metal ion binding / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 1
Function and homology information
SourceXenopus laevis / African clawed frog / amphibia / African clawed frog /
MethodCryo EM / single particle reconstruction / 6 Å resolution
AuthorsLu W / Du J / Goehring A
CitationJournal: Science / Year: 2017
Title: Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation.
Authors: Wei Lü / Juan Du / April Goehring / Eric Gouaux
Abstract: -methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B ...-methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B receptor in the absence or presence of the GluN2B-specific allosteric modulator Ro 25-6981 (Ro), determined by cryogenic electron microscopy (cryo-EM). In the absence of Ro, the GluN2A and GluN2B amino-terminal domains (ATDs) adopt "closed" and "open" clefts, respectively. Upon binding Ro, the GluN2B ATD clamshell transitions from an open to a closed conformation. Consistent with a predominance of the GluN2A subunit in ion channel gating, the GluN2A subunit interacts more extensively with GluN1 subunits throughout the receptor, in comparison with the GluN2B subunit. Differences in the conformation of the pseudo-2-fold-related GluN1 subunits further reflect receptor asymmetry. The triheteromeric NMDAR structures provide the first view of the most common NMDA receptor assembly and show how incorporation of two different GluN2 subunits modifies receptor symmetry and subunit interactions, allowing each subunit to uniquely influence receptor structure and function, thus increasing receptor complexity.
Copyright: 2017, American Association for the Advancement of Science.
Validation ReportPDB-ID: 5up2

SummaryFull reportAbout validation report
DateDeposition: Feb 1, 2017 / Header (metadata) release: Mar 22, 2017 / Map release: Mar 22, 2017 / Last update: Nov 8, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5up2
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5up2
  • Imaged by Jmol
  • Download
3D viewer
Supplemental images

Downloads & links

-
Map

Fileemd_8581.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.7 Å/pix.
= 435.2 Å
256 pix
1.7 Å/pix.
= 435.2 Å
256 pix
1.7 Å/pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.7 Å
Density
Contour Level:0.055 (by author), 0.055 (movie #1):
Minimum - Maximum-0.024976106 - 0.12082201
Average (Standard dev.)0.00058212783 (0.006057551)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 435.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0250.1210.001

-
Supplemental data

-
Sample components

+
Entire membrane protein

EntireName: membrane protein / Number of components: 6

+
Component #1: protein, membrane protein

ProteinName: membrane protein / Recombinant expression: No
SourceSpecies: Xenopus laevis
Source (engineered)Expression System: Homo sapiens

+
Component #2: protein, N-methyl-D-aspartate receptor subunit NR1-8a

ProteinName: N-methyl-D-aspartate receptor subunit NR1-8a / Recombinant expression: No
MassTheoretical: 94.056859 kDa
SourceSpecies:
Source (engineered)Expression System: Xenopus laevis

+
Component #3: protein, N-methyl-D-aspartate receptor subunit NR2A

ProteinName: N-methyl-D-aspartate receptor subunit NR2A / Recombinant expression: No
MassTheoretical: 93.535227 kDa
SourceSpecies:
Source (engineered)Expression System: Xenopus laevis

+
Component #4: protein, Ionotropic glutamate receptor subunit NR2B

ProteinName: Ionotropic glutamate receptor subunit NR2B / Recombinant expression: No
MassTheoretical: 94.552234 kDa
SourceSpecies:
Source (engineered)Expression System: Xenopus laevis

+
Component #5: protein, GluN2B-specific Fab, termed 11D1

ProteinName: GluN2B-specific Fab, termed 11D1 / Recombinant expression: No
MassTheoretical: 18.400619 kDa
SourceSpecies:
Source (engineered)Expression System: Mus musculus

+
Component #6: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.221208 kDa
SourceSpecies:

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.84 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 302052
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more