5UN1 | pdb_00005un1

Crystal structure of GluN1/GluN2B delta-ATD NMDA receptor

PDB DOI: https://doi.org/10.2210/pdb5UN1/pdb

Classification: MEMBRANE PROTEINS/INHIBITOR
Organism(s): Xenopus laevis
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2017-01-30 Released: 2018-02-07
Deposition Author(s): Song, X., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.316 (Depositor), 0.321 (DCC)
R-Value Work:
0.288 (Depositor), 0.291 (DCC)
R-Value Observed:
0.289 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Mechanism of NMDA receptor channel block by MK-801 and memantine.

Song, X., Jensen, M.O., Jogini, V., Stein, R.A., Lee, C.H., Mchaourab, H.S., Shaw, D.E., Gouaux, E.

(2018) Nature 556: 515-519

PubMed: 29670280 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-018-0039-9
Primary Citation Related Structures:
5UN1

PubMed Abstract:
The NMDA (N-methyl-D-aspartate) receptor transduces the binding of glutamate and glycine, coupling it to the opening of a calcium-permeable ion channel ¹ . Owing to the lack of high-resolution structural studies of the NMDA receptor, the mechanism by which ion-channel blockers occlude ion permeation is not well understood. Here we show that removal of the amino-terminal domains from the GluN1-GluN2B NMDA receptor yields a functional receptor and crystals with good diffraction properties, allowing us to map the binding site of the NMDA receptor blocker, MK-801. This crystal structure, together with long-timescale molecular dynamics simulations, shows how MK-801 and memantine (a drug approved for the treatment of Alzheimer's disease) bind within the vestibule of the ion channel, promote closure of the ion channel gate and lodge between the M3-helix-bundle crossing and the M2-pore loops, physically blocking ion permeation.

Organizational Affiliation

Vollum Institute, Oregon Health & Science University, Portland, OR, USA.

Macromolecule Content

Total Structure Weight: 408.4 kDa
Atom Count: 20,143
Modeled Residue Count: 3,294
Deposited Residue Count: 3,596
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-methyl-D-aspartate receptor subunit NR1-3a	A [auth G], B [auth A], E, G [auth C]	451	Xenopus laevis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis) Explore A0A1L8F5J9 Go to UniProtKB: A0A1L8F5J9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L8F5J9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ionotropic glutamate receptor subunit NR2B	C [auth B], D [auth H], F, H [auth D]	448	Xenopus laevis	Mutation(s): 0 Gene Names: NR2B, XELAEV_18025529mg Membrane Entity: Yes
UniProt
Find proteins for A7XY94 (Xenopus laevis) Explore A7XY94 Go to UniProtKB: A7XY94
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7XY94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain V [auth E] MOL2 format, chain V [auth E] mmCIF format, chain V [auth E]	V [auth E]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain V [auth E] Interactions & Density Focus chain V [auth E]
BMK Query on BMK Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain M [auth G] MOL2 format, chain S [auth B] MOL2 format, chain M [auth G] mmCIF format, chain S [auth B] mmCIF format, chain M [auth G]	M [auth G], S [auth B]	(5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene C₁₆ H₁₅ N LBOJYSIDWZQNJS-CVEARBPZSA-N		Interactions Focus chain M [auth G] Focus chain S [auth B] Interactions & Density Focus chain M [auth G] Focus chain S [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain U [auth H] SDF format, chain W [auth F] SDF format, chain X [auth D] SDF format, chain Z [auth D] SDF format, chain J [auth G] MOL2 format, chain R [auth B] MOL2 format, chain U [auth H] MOL2 format, chain W [auth F] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain J [auth G] mmCIF format, chain R [auth B] mmCIF format, chain U [auth H] mmCIF format, chain W [auth F] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain J [auth G]	J [auth G] R [auth B] U [auth H] W [auth F] X [auth D] J [auth G], R [auth B], U [auth H], W [auth F], X [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth G] Focus chain R [auth B] Focus chain U [auth H] Focus chain W [auth F] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain J [auth G] Focus chain R [auth B] Focus chain U [auth H] Focus chain W [auth F] Focus chain X [auth D] Focus chain Z [auth D]
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain N [auth G] SDF format, chain Q [auth B] SDF format, chain T [auth H] SDF format, chain Y [auth D] SDF format, chain L [auth G] MOL2 format, chain N [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain L [auth G] mmCIF format, chain N [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth H] mmCIF format, chain Y [auth D] mmCIF format, chain L [auth G]	L [auth G], N [auth G], Q [auth B], T [auth H], Y [auth D]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain L [auth G] Focus chain N [auth G] Focus chain Q [auth B] Focus chain T [auth H] Focus chain Y [auth D] Interactions & Density Focus chain L [auth G] Focus chain N [auth G] Focus chain Q [auth B] Focus chain T [auth H] Focus chain Y [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain K [auth G] MOL2 format, chain K [auth G] mmCIF format, chain K [auth G]	K [auth G]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain K [auth G] Interactions & Density Focus chain K [auth G]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain I [auth G] MOL2 format, chain P [auth A] MOL2 format, chain I [auth G] mmCIF format, chain P [auth A] mmCIF format, chain I [auth G]	I [auth G], P [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain I [auth G] Focus chain P [auth A] Interactions & Density Focus chain I [auth G] Focus chain P [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
BMK	BindingDB: 5UN1	Ki: min: 9, max: 31 (nM) from 2 assay(s)
BMK	BindingDB: 5UN1	IC50: 29 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.316 (Depositor), 0.321 (DCC)
R-Value Work: 0.288 (Depositor), 0.291 (DCC)
R-Value Observed: 0.289 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.57	α = 90
b = 108.47	β = 111.44
c = 182.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-07

Deposition Author(s):

Song, X.

Gouaux, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01-NS038631

Revision History (Full details and data files)

Version 1.0: 2018-02-07
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references
Version 1.2: 2018-05-02
Changes: Data collection, Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2022-04-13
Changes: Author supporting evidence, Database references, Structure summary
Version 1.5: 2023-10-04
Changes: Data collection, Refinement description
Version 1.6: 2024-10-30
Changes: Structure summary