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Protein

Glutamate receptor ionotropic, NMDA 1

Gene

grin1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg2+ (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref. 11, PubMed:28232581). Sensitivity to glutamate and channel kinetics depend on the subunit composition (Probable).Curated8 Publications

Enzyme regulationi

Channel activity is modulated by zinc ions. The activity of the heterotetramer with grin2b is stimulated by micromolar levels of Zn2+ (PubMed:19524674). The activity of the heterotetramer with grin2a is inhibited by nanomolar levels of Zn2+ (Ref. 11).2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi67Zinc; via tele nitrogen1 Publication1
Metal bindingi94Zinc1 Publication1
Metal bindingi100Zinc1 Publication1
Binding sitei521GlycineBy similarity1
Binding sitei686GlycineBy similarity1
Binding sitei730GlycineBy similarity1

GO - Molecular functioni

Keywordsi

Molecular functionIon channel, Ligand-gated ion channel, Receptor
Biological processIon transport, Transport
LigandCalcium, Magnesium, Metal-binding, Zinc

Protein family/group databases

TCDBi1.A.10.1.12. the glutamate-gated ion channel (gic) family of neurotransmitter receptors.

Names & Taxonomyi

Protein namesi
Recommended name:
Glutamate receptor ionotropic, NMDA 1
Short name:
GluN1
Alternative name(s):
N-methyl-D-aspartate receptor subunit NR11 Publication
Short name:
NMD-R1
Gene namesi
Name:grin1Imported
OrganismiXenopus laevis (African clawed frog)Imported
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus
Proteomesi
  • UP000186698 Componentsi: Chromosome 8l, Unassembled WGS sequence

Organism-specific databases

XenbaseiXB-GENE-866327. grin1.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini21 – 557ExtracellularCuratedAdd BLAST537
Transmembranei558 – 578Helical1 PublicationAdd BLAST21
Topological domaini579 – 600CytoplasmicCuratedAdd BLAST22
Intramembranei601 – 622Discontinuously helical1 PublicationAdd BLAST22
Topological domaini623 – 628CytoplasmicCurated6
Transmembranei629 – 645Helical1 PublicationAdd BLAST17
Topological domaini646 – 810ExtracellularCuratedAdd BLAST165
Transmembranei811 – 831Helical1 PublicationAdd BLAST21
Topological domaini832 – 903CytoplasmicCuratedAdd BLAST72

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Postsynaptic cell membrane, Synapse

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 20Sequence analysisAdd BLAST20
ChainiPRO_000044220921 – 903Glutamate receptor ionotropic, NMDA 1Sequence analysisAdd BLAST883

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi61N-linked (GlcNAc...) asparagineCombined sources2 Publications1
Disulfide bondi79 ↔ 308Combined sources1 Publication
Glycosylationi203N-linked (GlcNAc...) asparagineCombined sources3 Publications1
Glycosylationi276N-linked (GlcNAc...) asparagineCombined sources3 Publications1
Glycosylationi300N-linked (GlcNAc...) asparagineCombined sources2 Publications1
Glycosylationi368N-linked (GlcNAc...) asparagineCombined sources1 Publication1
Disulfide bondi420 ↔ 452Combined sources1 Publication
Disulfide bondi436 ↔ 453Combined sources1 Publication
Disulfide bondi742 ↔ 796Combined sources1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

Heterotetramer (PubMed:27062927). Forms heterotetrameric channels composed of two zeta subunits (grin1), and two epsilon subunits (grin2a, grin2b, grin2c or grin2d) (in vitro) (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref. 11, PubMed:28232581). Does not form functional channels by itself (PubMed:16214956). In vivo, the subunit composition may depend on the expression levels of the different subunits (Probable).Curated9 Publications

Protein-protein interaction databases

DIPiDIP-59169N.
DIP-61036N.
IntActiA0A1L8F5J9. 1 interactor.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3QEKX-ray2.00A/B23-405[»]
3QELX-ray2.60A/C23-405[»]
3QEMX-ray3.00A/C23-405[»]
4TLLX-ray3.59A/C22-836[»]
4TLMX-ray3.77A/C22-836[»]
5B3JX-ray2.90A/B23-405[»]
5EWJX-ray2.77A/C23-408[»]
5EWLX-ray2.98A/C23-408[»]
5EWMX-ray2.76A/C23-408[»]
5IOUelectron microscopy7.00A/C23-836[»]
5IOVelectron microscopy7.50A/C23-836[»]
5IPQelectron microscopy13.50A/C23-836[»]
5IPRelectron microscopy14.10A/C23-836[»]
5IPSelectron microscopy13.50A/C23-836[»]
5IPTelectron microscopy14.10A/C23-836[»]
5IPUelectron microscopy15.40A/C23-836[»]
5IPVelectron microscopy9.25A/C23-836[»]
5TPWX-ray2.91A24-408[»]
5TPZX-ray3.10A23-405[»]
5TQ0X-ray2.70A24-408[»]
5TQ2X-ray3.29A24-408[»]
5UOWelectron microscopy4.50A/C23-836[»]
5UP2electron microscopy6.00A/C1-836[»]
SMRiA0A1L8F5J9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni514 – 516Glycine bindingBy similarity3
Regioni601 – 620Pore-forming1 PublicationAdd BLAST20

Domaini

A hydrophobic region that gives rise to the prediction of a transmembrane span does not cross the membrane, but is part of a discontinuously helical region that dips into the membrane and is probably part of the pore and of the selectivity filter.2 Publications

Sequence similaritiesi

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

HOVERGENiHBG052638.
KOiK05208.

Family and domain databases

InterProiView protein in InterPro
IPR001828. ANF_lig-bd_rcpt.
IPR018882. CaM-bd_C0_NMDA_rcpt_NR1.
IPR019594. Glu/Gly-bd.
IPR001508. Iono_rcpt_met.
IPR001320. Iontro_rcpt.
IPR028082. Peripla_BP_I.
PfamiView protein in Pfam
PF01094. ANF_receptor. 1 hit.
PF10562. CaM_bdg_C0. 1 hit.
PF00060. Lig_chan. 1 hit.
PF10613. Lig_chan-Glu_bd. 1 hit.
PRINTSiPR00177. NMDARECEPTOR.
SMARTiView protein in SMART
SM00918. Lig_chan-Glu_bd. 1 hit.
SM00079. PBPe. 1 hit.
SUPFAMiSSF53822. SSF53822. 1 hit.

Sequences (8)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 8 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: A0A1L8F5J9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGTMRLFLLA VLFLFSFARA GCDPKIVNIG AVLSTKKHEQ IFREAVNQAN
60 70 80 90 100
KRHFTRKIQL NATSVTHRPN AIQMALSVCE DLISSQVYAI LVSHPPAPTD
110 120 130 140 150
HLTPTPISYT AGFYRIPVIG LTTRMSIYSD KSIHLSFLRT VPPYSHQALV
160 170 180 190 200
WFEMMRLFNW NHVILIVSDD HEGRAAQKKL ETLLEEKESK ADKVLQFEPG
210 220 230 240 250
TKNLTALLLE AKELEARVII LSASEDDATA VYKSAAMLDM TGAGYVWLVG
260 270 280 290 300
EREISGSALR YAPDGIIGLQ LINGKNESAH ISDAVAVVAQ AIHELFEMEN
310 320 330 340 350
ITDPPRGCVG NTNIWKTGPL FKRVLMSSKY PDGVTGRIEF NEDGDRKFAN
360 370 380 390 400
YSIMNLQNRK LVQVGIFNGS YIIQNDRKII WPGGETERPQ GYQMSTRLKI
410 420 430 440 450
VTIHQEPFVY VRPTTSDGTC REEYTINGDP IKKVICNGPN ETIPGRPTVP
460 470 480 490 500
QCCYGFCVDL LIKLAREMNF TYEVHLVADG KFGTQERVNN SNKKEWNGMM
510 520 530 540 550
GELLSGQADM IVAPLTINNE RAQYIEFSKP FKYQGLTILV KKEIPRSTLD
560 570 580 590 600
SFMQPFQSTL WLLVGLSVHV VAVMLYLLDR FSPFGRFKVN SEEEEEDALT
610 620 630 640 650
LSSAMWFSWG VLLNSGIGEG APRSFSARIL GMVWAGFAMI IVASYTANLA
660 670 680 690 700
AFLVLDRPEE RITGINDPRL RNPSDKFIYA TVKQSSVDIY FRRQVELSTM
710 720 730 740 750
YRHMEKHNYE SAAEAIQAVR DNKLHAFIWD SAVLEFEASQ KCDLVTTGEL
760 770 780 790 800
FFRSGFGIGM RKDSPWKQNV SLNILKSHEN GFMEELDKTW VRYQECDSRS
810 820 830 840 850
NAPATLTFEN MAGVFMLVAG GIVAGIFLIF IEIAYKRHKD ARRKQMQLAF
860 870 880 890 900
AAVNVWRKNL QDRKSGRAEP DPKKKASFRS ITSTLASSFK RRRSSKDTVN

VVV
Length:903
Mass (Da):101,793
Last modified:March 15, 2017 - v1
Checksum:iE2612938C9125D76
GO
Isoform 2 (identifier: A0A1L8F5J9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     899-901: VNV → QYPPTDITGQLNLSDPSVST

Show »
Length:920
Mass (Da):103,596
Checksum:iCF2631A4826597F5
GO
Isoform 3 (identifier: A0A1L8F5J9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     189-189: S → SKSKKRNYENLDQLSYDNKRGP
     899-901: VNV → QYPPTDITGQLNLSDPSVST

Show »
Length:941
Mass (Da):106,132
Checksum:iF2291DCD2C0E9925
GO
Isoform 4 (identifier: A0A1L8F5J9-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     862-866: DRKSG → PGNIK
     867-903: Missing.

Show »
Length:866
Mass (Da):97,626
Checksum:i4A11A43A122EE867
GO
Isoform 5 (identifier: A0A1L8F5J9-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     189-189: S → SKSKKRNYENLDQLSYDNKRGP
     862-866: DRKSG → PGNIK
     867-903: Missing.

Show »
Length:887
Mass (Da):100,162
Checksum:i5D4C46D99603128F
GO
Isoform 6 (identifier: A0A1L8F5J9-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     189-189: S → SKSKKRNYENLDQLSYDNKRGP
     862-901: DRKSGRAEPDPKKKASFRSITSTLASSFKRRRSSKDTVNV → QYPPTDITGQLNLSDPSVST

Show »
Length:904
Mass (Da):101,966
Checksum:i8ACCA847F88D4A9D
GO
Isoform 7 (identifier: A0A1L8F5J9-7) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     862-901: DRKSGRAEPDPKKKASFRSITSTLASSFKRRRSSKDTVNV → QYPPTDITGQLNLSDPSVST

Show »
Length:883
Mass (Da):99,430
Checksum:iE46FE8F7CA85F883
GO
Isoform 8 (identifier: A0A1L8F5J9-8) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     186-189: EKES → GKESKSKKRNYENLDQLSYDNKRGP
     862-901: DRKSGRAEPDPKKKASFRSITSTLASSFKRRRSSKDTVNV → QYPPTDITGQLNLSDPSVST

Show »
Length:904
Mass (Da):101,894
Checksum:i46D8FE0EA6D903F2
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_059206186 – 189EKES → GKESKSKKRNYENLDQLSYD NKRGP in isoform 8. 4
Alternative sequenceiVSP_059207189S → SKSKKRNYENLDQLSYDNKR GP in isoform 3, isoform 5 and isoform 6. 1
Alternative sequenceiVSP_059208862 – 901DRKSG…DTVNV → QYPPTDITGQLNLSDPSVST in isoform 6, isoform 7 and isoform 8. Add BLAST40
Alternative sequenceiVSP_059209862 – 866DRKSG → PGNIK in isoform 4 and isoform 5. 5
Alternative sequenceiVSP_059210867 – 903Missing in isoform 4 and isoform 5. Add BLAST37
Alternative sequenceiVSP_059211899 – 901VNV → QYPPTDITGQLNLSDPSVST in isoform 2 and isoform 3. 3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X94081 mRNA. Translation: CAA63825.1.
X94156 mRNA. Translation: CAA63871.1.
DQ066918 mRNA. Translation: AAY63890.1.
FJ571597 mRNA. Translation: ACN87989.1.
FJ571598 mRNA. Translation: ACN87990.1.
FJ571599 mRNA. Translation: ACN87991.1.
FJ571600 mRNA. Translation: ACN87992.1.
FJ571601 mRNA. Translation: ACN87993.1.
CM004480 Genomic DNA. Translation: OCT66859.1.
RefSeqiNP_001081615.1. NM_001088146.1.
NP_001081616.1. NM_001088147.1.
UniGeneiXl.135.

Genome annotation databases

GeneIDi397953.
KEGGixla:397953.

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiNMDZ1_XENLA
AccessioniPrimary (citable) accession number: A0A1L8F5J9
Secondary accession number(s): C0KD15
, C0KD16, C0KD17, C0KD18, C0KD19, Q4PLR7, Q91805, Q91977
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2017
Last sequence update: March 15, 2017
Last modified: October 25, 2017
This is version 8 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families