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Title :   CRYSTAL STRUCTURE OF THE SECOND LNS/LG DOMAIN FROM NEUREXIN 1 ALPHA

Authors :   L. R. Sheckler, L. Henry, S. Sugita, T. C. Sudhof, G. Rudenko

Date :   14 May 06 (Deposition) - 20 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   B-Sandwich, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. R. Sheckler, L. Henry, S. Sugita, T. C. Sudhof, G. Rudenko
Crystal Structure Of The Second Lns/Lg Domain From Neurexin 1{Alpha}: Ca2+ Binding And The Effects Of Alternative Splicing
J. Biol. Chem. V. 281 22896 2006
PubMed-ID: 16772286 | Reference-DOI: 10.1074/JBC.M603464200

Molecule 1 - NEUREXIN-1-ALPHA
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SECOND LNS/LG DOMAIN (RESIDUES 295-476)
	Gene	:	NRXN1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	NEUREXIN I-ALPHA

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:329 , LEU A:346 , MSE A:414 , HOH A:5001 , HOH B:5056 , HOH B:5317	BINDING SITE FOR RESIDUE CA A 1000
2	AC2	SOFTWARE	ASP B:329 , LEU B:346 , MSE B:414 , HOH B:5027 , HOH B:5179 , HOH B:5234	BINDING SITE FOR RESIDUE CA B 2000
3	AC3	SOFTWARE	GLU B:356 , ASP C:329 , LEU C:346 , MSE C:414 , HOH C:5054 , HOH C:5346	BINDING SITE FOR RESIDUE CA C 3000
4	AC4	SOFTWARE	GLU A:356 , ASP D:329 , LEU D:346 , MSE D:414 , HOH D:5045 , HOH D:5347	BINDING SITE FOR RESIDUE CA D 4000
5	AC5	SOFTWARE	VAL A:355 , GLU A:356 , THR A:403 , THR A:404 , HOH A:5104 , GLN D:302 , HOH D:5423	BINDING SITE FOR RESIDUE GOL A 4500
6	AC6	SOFTWARE	ARG A:317 , ASN A:337 , LYS A:361 , HOH A:5057 , SER D:348 , GLU D:410	BINDING SITE FOR RESIDUE GOL D 4501
7	AC7	SOFTWARE	GLU B:356 , VAL B:358 , THR B:403 , THR B:404 , HOH B:5116 , HOH C:5346	BINDING SITE FOR RESIDUE GOL B 4502
8	AC8	SOFTWARE	PRO A:357 , VAL A:358 , ASN A:359 , LYS A:361 , ASP A:364 , HIS A:368 , ASP A:399	BINDING SITE FOR RESIDUE GOL A 4503

(no "SS Bond" information available for 2H0B)

(no "Cis Peptide Bond" information available for 2H0B)

(no "SAP(SNP)/Variant" information available for 2H0B)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	NRX1A_BOVIN	30-217 299-496 503-695 741-914 928-1103 1149-1347	4	- A:283-475 B:283-475 C:283-475 D:283-475 - - - -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	NRX1A_BOVIN	30-217 299-496 503-695 741-914 928-1103 1149-1347	1	- A:283-475 - - - - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	NRX1A_BOVIN	30-217 299-496 503-695 741-914 928-1103 1149-1347	1	- - B:283-475 - - - - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	NRX1A_BOVIN	30-217 299-496 503-695 741-914 928-1103 1149-1347	1	- - - C:283-475 - - - - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	NRX1A_BOVIN	30-217 299-496 503-695 741-914 928-1103 1149-1347	1	- - - - D:283-475 - - - -

(no "Exon" information available for 2H0B)

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:181
 aligned with NRX1A_BOVIN | Q28146 from UniProtKB/Swiss-Prot  Length:1530

    Alignment length:196
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      
          NRX1A_BOVIN   296 EEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQTSGIGHAMVNKLHCSVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEVVYKNNDVRLELSRLAKQGDPKMKIHGV 491
               SCOP domains d2h0ba_ A: Ligand-binding domain of neurexin 1beta                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeeee.....eee.eeeeeeeeee....eeeeee....eeeeeeee..eeeeeeee...eeeeee............eeeeeeee..e---------------eeeee....eeeee.......eee..eeee....hhhhh.........eeeeeeeeeee...eehhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LAM_G_DOMAIN  PDB: A:283-475 UniProt: 299-496                                                                                                                                                     PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h0b A 280 EEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLmLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQ---------------VTISVDGILTTTGYTQEDYTmLGSDDFFYVGGSPSTADLPGSPVSNNFmGCLKEVVYKNNDVRLELSRLAKQGDPKmKIHGV 475
                                   289       299       309       319 |     329       339       349       359       369        |-         -    |  399       409    |  419       429       439  |    449       459       469|     
                                                                   321-MSE                                                  378             394                 414-MSE                     442-MSE                     470-MSE

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with NRX1A_BOVIN | Q28146 from UniProtKB/Swiss-Prot  Length:1530

    Alignment length:196
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      
          NRX1A_BOVIN   296 EEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQTSGIGHAMVNKLHCSVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEVVYKNNDVRLELSRLAKQGDPKMKIHGV 491
               SCOP domains d2h0bb_ B: Ligand-binding domain of neurexin 1beta                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeeee.....eee.eeeeeeeeee....eeeeee....eeeeeeee..eeeeeeee....eeeee............eeeeeeee..e---------------eeeee....eeeee.......eee..eeee....hhhhh.........eeeeeeeeeee...eeehhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LAM_G_DOMAIN  PDB: B:283-475 UniProt: 299-496                                                                                                                                                     PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h0b B 280 EEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLmLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQ---------------VTISVDGILTTTGYTQEDYTmLGSDDFFYVGGSPSTADLPGSPVSNNFmGCLKEVVYKNNDVRLELSRLAKQGDPKmKIHGV 475
                                   289       299       309       319 |     329       339       349       359       369        |-         -    |  399       409    |  419       429       439  |    449       459       469|     
                                                                   321-MSE                                                  378             394                 414-MSE                     442-MSE                     470-MSE

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with NRX1A_BOVIN | Q28146 from UniProtKB/Swiss-Prot  Length:1530

    Alignment length:198
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483        
          NRX1A_BOVIN   294 GKEEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQTSGIGHAMVNKLHCSVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEVVYKNNDVRLELSRLAKQGDPKMKIHGV 491
               SCOP domains d2h0bc_ C: Ligand-binding domain of neurexin 1beta                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....eeee.....eee.eeeeeeeeee....eeeeee....eeeeeeee..eeeeeeee...eeeeee............eeeeeeee..e---------------eeeee....eeeee.......eee..eeee....hhhhh..........eeeeeeeeee...eehhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----LAM_G_DOMAIN  PDB: C:283-475 UniProt: 299-496                                                                                                                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h0b C 278 SKEEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLmLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQ---------------VTISVDGILTTTGYTQEDYTmLGSDDFFYVGGSPSTADLPGSPVSNNFmGCLKEVVYKNNDVRLELSRLAKQGDPKmKIHGV 475
                                   287       297       307       317   |   327       337       347       357       367       377|        -      |397       407      |417       427       437    |  447       457       467  |     
                                                                     321-MSE                                                  378             394                 414-MSE                     442-MSE                     470-MSE

Chain D from PDB  Type:PROTEIN  Length:182
 aligned with NRX1A_BOVIN | Q28146 from UniProtKB/Swiss-Prot  Length:1530

    Alignment length:197
                                   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
          NRX1A_BOVIN   295 KEEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQTSGIGHAMVNKLHCSVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEVVYKNNDVRLELSRLAKQGDPKMKIHGV 491
               SCOP domains d2h0bd_ D: Ligand-binding domain of neurexin 1beta                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeee......eee.eeeeeeeeee....eeeeee....eeeeeeee..eeeeeeee....eeeee............eeeeeeee..e---------------eeeee....eeeee.......eee....ee....hhhhh.........eeeeeeeeeee...eeehhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LAM_G_DOMAIN  PDB: D:283-475 UniProt: 299-496                                                                                                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h0b D 279 KEEYIATFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLmLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQ---------------VTISVDGILTTTGYTQEDYTmLGSDDFFYVGGSPSTADLPGSPVSNNFmGCLKEVVYKNNDVRLELSRLAKQGDPKmKIHGV 475
                                   288       298       308       318  |    328       338       348       358       368       378         -     | 398       408     | 418       428       438   |   448       458       468 |     
                                                                    321-MSE                                                  378             394                 414-MSE                     442-MSE                     470-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Laminin G-like module (37)

Protein domain: Ligand-binding domain of neurexin 1beta (7)

Cow (Bos taurus) [TaxId: 9913] (1)

1a	d2h0ba_	A:
1b	d2h0bb_	B:
1c	d2h0bc_	C:
1d	d2h0bd_	D:

(no "CATH Domain" information available for 2H0B)

(no "Pfam Domain" information available for 2H0B)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NRX1A_BOVIN | Q28146)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0097109	neuroligin family protein binding	Interacting selectively and non-covalently with a member of the neuroligin protein family, neuronal cell surface proteins that mediate synapse formation.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
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:0042734	presynaptic membrane	A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma 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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	2h0b
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	NRX1A_BOVIN \| Q28146	:	2r16 3asi 3poy 3qcw 3r05

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Ligands, Modified Residues, Ions (3, 24)

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