2WIM - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NCAM2 IG1-3

Authors :   N. Kulahin, O. Kristensen, K. Rasmussen, J. Kastrup, V. Berezin, E. Boc P. Walmod, M. Gajhede

Date :   13 May 09 (Deposition) - 25 Aug 10 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Cell Membrane, Cell Adhesion, Transmembrane, Immunoglobulin Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Kulahin, O. Kristensen, K. K. Rasmussen, L. Olsen, P. Rydberg, B. Vestergaard, J. S. Kastrup, V. Berezin, E. Bock, P. S. Walmod, M. Gajhede
Structural Model And Trans-Interaction Of The Entire Ectodomain Of The Olfactory Cell Adhesion Molecule.
Structure V. 19 203 2011
PubMed-ID: 21300289 | Reference-DOI: 10.1016/J.STR.2010.12.014

Molecule 1 - NEURAL CELL ADHESION MOLECULE 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Fragment	:	IGI-III, RESIDUES 19-301
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	N-CAM 2, NCAM2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:128 , ASN A:177 , LYS A:178 , SER A:179	BINDING SITE FOR RESIDUE NDG A 950
2	AC2	SOFTWARE	SER A:217 , ASN A:219	BINDING SITE FOR RESIDUE NAG A 951
3	AC3	SOFTWARE	ASN B:219	BINDING SITE FOR RESIDUE NDG B 953
4	AC4	SOFTWARE	SER A:37	BINDING SITE FOR RESIDUE CA A1299

Asymmetric Unit

No.	Residues
1	A:42	-	A:93
2	A:136	-	A:186
3	A:232	-	A:281
4	B:42	-	B:93
5	B:136	-	B:186
6	B:232	-	B:281

Asymmetric Unit

No.	Residues
1	Ser A:237	-	Pro A:238
2	Ser B:122	-	Pro B:123
3	Ser B:141	-	Pro B:142
4	Ser B:237	-	Pro B:238

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

(no "PROSITE Motif" information available for 2WIM)

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000400546	1	ENSE00001543472	chr21:22370633-22370936	304	NCAM2_HUMAN	1-19	19	2	A:19-19 B:19-19	1 1
1.6	ENST00000400546	6	ENSE00001017047	chr21:22652898-22652972	75	NCAM2_HUMAN	19-44	26	2	A:19-44 B:19-44	26 26
1.7	ENST00000400546	7	ENSE00001017039	chr21:22656514-22656720	207	NCAM2_HUMAN	44-113	70	2	A:44-113 B:44-113	70 70
1.8	ENST00000400546	8	ENSE00001017049	chr21:22658589-22658732	144	NCAM2_HUMAN	113-161	49	2	A:113-161 (gaps) B:113-161 (gaps)	49 49
1.10b	ENST00000400546	10b	ENSE00001017037	chr21:22664424-22664561	138	NCAM2_HUMAN	161-207	47	2	A:161-207 B:161-207	47 47
1.11	ENST00000400546	11	ENSE00001017040	chr21:22696703-22696820	118	NCAM2_HUMAN	207-246	40	2	A:207-246 B:207-246 (gaps)	40 40
1.12	ENST00000400546	12	ENSE00001017034	chr21:22707825-22707985	161	NCAM2_HUMAN	246-300	55	2	A:246-298 B:246-294 (gaps)	53 49
1.13b	ENST00000400546	13b	ENSE00001017033	chr21:22710709-22710854	146	NCAM2_HUMAN	300-348	49	0	-	-
1.14b	ENST00000400546	14b	ENSE00001017041	chr21:22746183-22746333	151	NCAM2_HUMAN	349-399	51	0	-	-
1.15	ENST00000400546	15	ENSE00001017045	chr21:22782594-22782781	188	NCAM2_HUMAN	399-461	63	0	-	-
1.16	ENST00000400546	16	ENSE00001017052	chr21:22790793-22790889	97	NCAM2_HUMAN	462-494	33	0	-	-
1.17	ENST00000400546	17	ENSE00001017031	chr21:22804428-22804601	174	NCAM2_HUMAN	494-552	59	0	-	-
1.19	ENST00000400546	19	ENSE00001017043	chr21:22838927-22839046	120	NCAM2_HUMAN	552-592	41	0	-	-
1.20	ENST00000400546	20	ENSE00001017051	chr21:22840983-22841104	122	NCAM2_HUMAN	592-632	41	0	-	-
1.21	ENST00000400546	21	ENSE00001017035	chr21:22849612-22849792	181	NCAM2_HUMAN	633-693	61	0	-	-
1.22	ENST00000400546	22	ENSE00001017048	chr21:22881172-22881376	205	NCAM2_HUMAN	693-761	69	0	-	-
1.23	ENST00000400546	23	ENSE00001017044	chr21:22906858-22906977	120	NCAM2_HUMAN	761-801	41	0	-	-
1.24b	ENST00000400546	24b	ENSE00001543443	chr21:22910167-22915650	5484	NCAM2_HUMAN	801-837	37	0	-	-

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:276
 aligned with NCAM2_HUMAN | O15394 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:280
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
          NCAM2_HUMAN    19 ALLQVTISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNANIEDAGIYRCQATDAKGQTQEATVVLEIYQKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYHNEEVTTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQAFLQV 298
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wimA01 A:19-112 Immunoglobulins                                                              2wimA02 A:113-208 Immunoglobulins                                                               2wimA03 A:209-298 Immunoglobulins                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeee....eeeeeeee....eee..............eeeeee..eeeeee...hhhhheeeeeeee.....eeeeeeeeeee...........eeee....eee..........eeeee..----.......eee.....eee...hhhhheeeeeeee......eeeeeeeeeee..........eee.......eeeee.........eeeeee..ee......eee.....eeeee.......eeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1------------------------Exon 1.7  PDB: A:44-113 UniProt: 44-113                               -----------------------------------------------Exon 1.10b  PDB: A:161-207 UniProt: 161-207    --------------------------------------Exon 1.12  PDB: A:246-298 UniProt: 246-300            Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: A:19-44    --------------------------------------------------------------------Exon 1.8  PDB: A:113-161 (gaps) UniProt: 113-161 ---------------------------------------------Exon 1.11  PDB: A:207-246               ---------------------------------------------------- Transcript 1 (2)
                 2wim A  19 ALLQVTISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNANIEDAGIYRCQATDAKGQTQEATVVLEIYQKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYH----TTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQAFLQV 298
                                    28        38        48        58        68        78        88        98       108       118       128       138       148  |    158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
                                                                                                                                                              151  156

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with NCAM2_HUMAN | O15394 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:276
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288      
          NCAM2_HUMAN    19 ALLQVTISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNANIEDAGIYRCQATDAKGQTQEATVVLEIYQKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYHNEEVTTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQA 294
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wimB01 B:19-112 Immunoglobulins                                                              2wimB02 B:113-208 Immunoglobulins                                                               2wimB03 B:2     09-294 Immunoglobulins                                                 CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------    -------------------------------------------------------I-set-2wi     mB01 B:211-294                                                         Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------    -------------------------------------------------------I-set-2wi     mB02 B:211-294                                                         Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------    -------------------------------------------------------I-set-2wi     mB03 B:211-294                                                         Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------    -------------------------------------------------------I-set-2wi     mB04 B:211-294                                                         Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------------    -------------------------------------------------------I-set-2wi     mB05 B:211-294                                                         Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------------------------------------------------------------    -------------------------------------------------------I-set-2wi     mB06 B:211-294                                                         Pfam domains (6)
         Sec.struct. author ...eeee...eeeee....eeeeeeee....eeeee............eeeeee..eeeeee...hhhhheeeeeeee.....eeeeeeeeeee...ee......eeee...eeee...ee.....eeeee..----.......eee.....eeeee......eeeeeeeee....eeeeeeeeeeeeeeeeee.......-----....eee.eeeee......eee..ee..............eee.----.......ee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1------------------------Exon 1.7  PDB: B:44-113 UniProt: 44-113                               -----------------------------------------------Exon 1.10b  PDB: B:161-207 UniProt: 161-207    --------------------------------------Exon 1.12  PDB: B:246-294 (gaps) UniProt: 246-300 Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: B:19-44    --------------------------------------------------------------------Exon 1.8  PDB: B:113-161 (gaps) UniProt: 113-161 ---------------------------------------------Exon 1.11  PDB: B:207-246 (gaps)        ------------------------------------------------ Transcript 1 (2)
                 2wim B  19 ALLQVTISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNANIEDAGIYRCQATDAKGQTQEATVVLEIYQKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYH----TTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFN-----GEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTV----NSDGGPYVCRATNKAGEDEKQA 294
                                    28        38        48        58        68        78        88        98       108       118       128       138       148  |    158       168       178       188       198       208       218|     |228       238       248       258       268    |  278       288      
                                                                                                                                                              151  156                                                            219   225                                        268  273

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 2WIM)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	2wimA01	A:19-112
1b	2wimB01	B:19-112
1c	2wimA02	A:113-208
1d	2wimB02	B:113-208
1e	2wimA03	A:209-298
1f	2wimB03	B:209-294

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: I-set (67)

Homo sapiens (Human) (50)

1a	I-set-2wimB01	B:211-294
1b	I-set-2wimB02	B:211-294
1c	I-set-2wimB03	B:211-294
1d	I-set-2wimB04	B:211-294
1e	I-set-2wimB05	B:211-294
1f	I-set-2wimB06	B:211-294

Asymmetric Unit(hide GO term definitions)

Chain A,B (NCAM2_HUMAN | O15394)

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.
	GO:0007158	neuron cell-cell adhesion	The attachment of a neuron to another cell via adhesion molecules.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:237 - Pro A:238	[ RasMol ]
		Ser B:122 - Pro B:123	[ RasMol ]
		Ser B:141 - Pro B:142	[ RasMol ]
		Ser B:237 - Pro B:238	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	NCAM2_HUMAN \| O15394	:	2doc 2jll 2kbg 2v5t 2vaj 2xy1 2xy2 2xyc

2doc	SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-III DOMAIN OFHUMAN NEURAL CELL ADHESION MOLECULE 2
2jll	CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3II
2v5t	CRYSTAL STRUCTURE OF NCAM2 IG2-3
2vaj	CRYSTAL STRUCTURE OF NCAM2 IG1 (I4122 CELL UNIT)
2xy1	CRYSTAL STRUCTURE OF NCAM2 IG3-4
2xy2	CRYSTAL STRUCTURE OF NCAM2 IG1-2
2xyc	CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3I

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Ligands, Modified Residues, Ions (3, 4)

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SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

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Exons (7, 14)

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