3QEK - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAIN OF THE NMDA RECEPTOR SUBUNIT GLUN1

Authors :   E. Karakas, N. Simorowski, H. Furukawa

Date :   20 Jan 11 (Deposition) - 15 Jun 11 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Amino Terminal Domain, Ion Channel, Nmda Receptor, Allosteric Modulation, Phenylethanolamine, Polyamine, Extracellular, Membrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Karakas, N. Simorowski, H. Furukawa
Subunit Arrangement And Phenylethanolamine Binding In Glun1/Glun2B Nmda Receptors.
Nature V. 475 249 2011
PubMed-ID: 21677647 | Reference-DOI: 10.1038/NATURE10180

Molecule 1 - NMDA GLUTAMATE RECEPTOR SUBUNIT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	AMINO TERMINAL DOMAIN, RESIDUES 23-405
	Gene	:	GRIN1, NR1
	Mutation	:	YES
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 27)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	K	2	Ligand/Ion	POTASSIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
4	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 11)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (3, 25)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
4	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:128 , ASP A:130 , ILE A:133 , HIS A:134 , HOH A:522	BINDING SITE FOR RESIDUE K A 501
2	AC2	SOFTWARE	ASN A:297 , ALA A:300 , HOH A:542	BINDING SITE FOR RESIDUE NAG A 502
3	AC3	SOFTWARE	GLU A:320 , ASN A:321	BINDING SITE FOR RESIDUE NAG A 503
4	AC4	SOFTWARE	ASN A:389 , NAG A:505	BINDING SITE FOR RESIDUE NAG A 504
5	AC5	SOFTWARE	TYR A:392 , NAG A:504 , BMA A:506 , ASN B:159	BINDING SITE FOR RESIDUE NAG A 505
6	AC6	SOFTWARE	NAG A:505 , ARG B:156 , ASN B:159	BINDING SITE FOR RESIDUE BMA A 506
7	AC7	SOFTWARE	TYR B:128 , ASP B:130 , ILE B:133 , HIS B:134 , HOH B:510	BINDING SITE FOR RESIDUE K B 501
8	AC8	SOFTWARE	LYS B:214 , ASN B:297 , VAL B:355	BINDING SITE FOR RESIDUE NAG B 502
9	AC9	SOFTWARE	ASN B:389 , TYR B:392 , ILE B:394	BINDING SITE FOR RESIDUE NAG B 503

Asymmetric Unit

No.	Residues
1	A:79	-	A:329
2	B:79	-	B:329

(no "Cis Peptide Bond" information available for 3QEK)

(no "SAP(SNP)/Variant" information available for 3QEK)

(no "PROSITE Motif" information available for 3QEK)

(no "Exon" information available for 3QEK)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:361
 aligned with Q91977_XENLA | Q91977 from UniProtKB/TrEMBL  Length:904

    Alignment length:383
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402   
         Q91977_XENLA    23 DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLNATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFANYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGG 405
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee..--------.hhhhhhhhhh....eee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh--------------...........eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.......eee..hhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhh..eeee..eee............eeeeeee..eeeeeeee....eee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qek A  23 DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQmALSVCEDLISSQVYAILVSH--------TPTPISYTAGFYRIPVIGLTTRmSIYSDKSIHLSFLRTVPPYSHQALVWFEmmRLFNWNHVILIVSDDHEGRAAQKKLETLLE--------------DQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAmLDmTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEmENITDPPRGCVGNTNIWKTGPLFKRVLmSSKYPDGVTGRIEFNEDGDRKFAQYSImNLQNRKLVQVGIFNGSYIIQNDRKIIWPGG 405
                                    32        42        52        62        72 |      82        92 |       -|      112       122  |    132       142       152 ||    162       172       182  |      -       202       212       222       232       242       252     | 262       272       282       292       302       312      |322       332       342    |  352       362       372  |    382       392       402   
                                                                              74-MSE              94      103                   125-MSE                      154-MSE                        185            200                                                       258-MSE                                                      319-MSE                     347-MSE                     375-MSE                          
                                                                                                                                                              155-MSE                                                                                                   261-MSE

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with Q91977_XENLA | Q91977 from UniProtKB/TrEMBL  Length:904

    Alignment length:382
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403  
         Q91977_XENLA    24 PKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLNATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFANYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGG 405
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------ANF_receptor-3qek    B01 B:37-378                                                                                                                                                                                                                                                                                                                     --------------------------- Pfam domains (1)
           Pfam domains (2) -------------ANF_receptor-3qek    B02 B:37-378                                                                                                                                                                                                                                                                                                                     --------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhhhhhhhhh----.eeeeeeee...hhhhhhhhhhhhhhhh.eeeeee...-------.hhhhhhhhhh....eee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.-------------.eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh..eeee..eee............eeeeeee..eeeeeeee....eee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qek B  24 PKIVNIGAVLSTKKHEQIFREAVNQANKRH----IQLQATSVTHRPNAIQmALSVCEDLISSQVYAILVSHP-------TPTPISYTAGFYRIPVIGLTTRmSIYSDKSIHLSFLRTVPPYSHQALVWFEmmRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNY-------------PKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAmLDmTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEmENITDPPRGCVGNTNIWKTGPLFKRVLmSSKYPDGVTGRIEFNEDGDRKFAQYSImNLQNRKLVQVGIFNGSYIIQNDRKIIWPGG 405
                                    33        43        53    |   63        73|       83        93 |     103       113       123 |     133       143       153||     163       173       183       193  |      -      |213       223       233       243       253    |  263       273       283       293       303       313     | 323       333       343   |   353       363       373 |     383       393       403  
                                                        53   58              74-MSE               95     103                   125-MSE                      154-MSE                                   196           210                                             258-MSE                                                      319-MSE                     347-MSE                     375-MSE                          
                                                                                                                                                             155-MSE                                                                                                   261-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3QEK)

(no "CATH Domain" information available for 3QEK)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: ANF_receptor (21)

Xenopus laevis (African clawed frog) (3)

1a	ANF_receptor-3qekB01	B:37-378
1b	ANF_receptor-3qekB02	B:37-378

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q91977_XENLA | Q91977)

molecular function
	GO:0005234	extracellular-glutamate-gated ion channel activity	Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts.
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0004970	ionotropic glutamate receptor activity	Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0035235	ionotropic glutamate receptor signaling pathway	A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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	Cis Peptide Bonds
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	3qek
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	Q91977_XENLA \| Q91977
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	Q91977_XENLA \| Q91977	:	3qel 3qem 5b3j 5ewj 5ewl 5ewm 5tpw 5tpz 5tq0 5tq2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 27)

Sites (9, 9)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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