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Title :   CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3II

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

Date :   10 Sep 08 (Deposition) - 17 Nov 09 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Immunoglobulin Domain, Immunoglobulin Superfamily, Cell Adhesion, Transmembrane, Phosphoprotein, Neural, Membrane, Glycoprotein, Cell Membrane (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
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	KM71H
	Expression System Taxid	:	4922
	Expression System Vector	:	PPICZALFAC
	Fragment	:	IGIV-FN3II, RESIDUES 301-689
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NCAM2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:419 , GLU A:461 , GLN A:531 , GLN A:577 , HOH A:2144 , HOH A:2145 , HOH A:2146	BINDING SITE FOR RESIDUE NAG A1690
2	AC2	SOFTWARE	LEU A:439 , ASN A:445 , ASN A:558	BINDING SITE FOR RESIDUE NAG A1691
3	AC3	SOFTWARE	ASP A:437 , ARG A:472 , ASN A:474 , PHE A:485 , GLU A:487	BINDING SITE FOR RESIDUE NAG A1692
4	AC4	SOFTWARE	ASN A:309 , TYR A:394	BINDING SITE FOR RESIDUE NAG A1693
5	AC5	SOFTWARE	ASP A:579 , GLU A:681 , CA A:1695 , HOH A:2084 , HOH A:2147	BINDING SITE FOR RESIDUE GOL A1694
6	AC6	SOFTWARE	ASP A:494 , GLU A:681 , GOL A:1694 , HOH A:2084 , HOH A:2147	BINDING SITE FOR RESIDUE CA A1695

Asymmetric/Biological Unit

No.	Residues
1	A:322	-	A:380
2	A:422	-	A:475

Asymmetric/Biological Unit

No.	Residues
1	Glu A:327	-	Pro A:328
2	Lys A:348	-	Ser A:349
3	Asn A:427	-	Pro A:428
4	Leu A:441	-	Pro A:442
5	Ser A:605	-	Gly A:606

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047898	L	350	P	NCAM2_HUMAN	Polymorphism	232518	A	L	350	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	NCAM2_HUMAN	498-591 593-688	2	A:498-591 A:593-688

Asymmetric/Biological Unit (8, 8)

	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	0	-	-
1.6	ENST00000400546	6	ENSE00001017047	chr21:22652898-22652972	75	NCAM2_HUMAN	19-44	26	0	-	-
1.7	ENST00000400546	7	ENSE00001017039	chr21:22656514-22656720	207	NCAM2_HUMAN	44-113	70	0	-	-
1.8	ENST00000400546	8	ENSE00001017049	chr21:22658589-22658732	144	NCAM2_HUMAN	113-161	49	0	-	-
1.10b	ENST00000400546	10b	ENSE00001017037	chr21:22664424-22664561	138	NCAM2_HUMAN	161-207	47	0	-	-
1.11	ENST00000400546	11	ENSE00001017040	chr21:22696703-22696820	118	NCAM2_HUMAN	207-246	40	0	-	-
1.12	ENST00000400546	12	ENSE00001017034	chr21:22707825-22707985	161	NCAM2_HUMAN	246-300	55	0	-	-
1.13b	ENST00000400546	13b	ENSE00001017033	chr21:22710709-22710854	146	NCAM2_HUMAN	300-348	49	1	A:301-348 (gaps)	48
1.14b	ENST00000400546	14b	ENSE00001017041	chr21:22746183-22746333	151	NCAM2_HUMAN	349-399	51	1	A:349-399	51
1.15	ENST00000400546	15	ENSE00001017045	chr21:22782594-22782781	188	NCAM2_HUMAN	399-461	63	1	A:399-461	63
1.16	ENST00000400546	16	ENSE00001017052	chr21:22790793-22790889	97	NCAM2_HUMAN	462-494	33	1	A:462-494	33
1.17	ENST00000400546	17	ENSE00001017031	chr21:22804428-22804601	174	NCAM2_HUMAN	494-552	59	1	A:494-552	59
1.19	ENST00000400546	19	ENSE00001017043	chr21:22838927-22839046	120	NCAM2_HUMAN	552-592	41	1	A:552-592	41
1.20	ENST00000400546	20	ENSE00001017051	chr21:22840983-22841104	122	NCAM2_HUMAN	592-632	41	1	A:592-632	41
1.21	ENST00000400546	21	ENSE00001017035	chr21:22849612-22849792	181	NCAM2_HUMAN	633-693	61	1	A:638-689	52
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/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:382
 aligned with NCAM2_HUMAN | O15394 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:389
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680         
          NCAM2_HUMAN   301 QPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISNQTIYYSWEGNPINISCDVKSNPPASIHWRRDKLVLPAKNTTNLKTYSTGRKMILEIAPTSDNDFGRYNCTATNHIGTRFQEYILALADVPSSPYGVKIIELSQTTAKVSFNKPDSHGGVPIHHYQVDVKEVASEIWKIVRSHGVQTMVVLNNLEPNTTYEIRVAAVNGKGQGDYSKIEIFQTLPVREPSPPSIHGQPSSGKSFKLSITKQDDGGAPILEYIVKYRSKDKEDQWLEKKVQGNKDHIILEHLQWTMGYEVQITAANRLGYSEPTVYEFSMPPKPN 689
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2jllA04 A:593-689 Immunoglobulins                                                                 CATH domains
           Pfam domains (1) ---------------------------------------------  -----------------------------------------------------I-set-2jllA03 A:401-492                                                                     ----------------------------------------------------------------------------------------------------fn3-2jllA01 A:593-678                                                                 ----------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------  -----------------------------------------------------I-set-2jllA04 A:401-492                                                                     ----------------------------------------------------------------------------------------------------fn3-2jllA02 A:593-678                                                                 ----------- Pfam domains (2)
         Sec.struct. author ..eeee...eeee...eeeeeeeee.....eeeeee....eee..--......eeeee...eeeeeee..hhhhheeeeeeee....eeeeeeeeeeeeeeee.....eeee.....eeeee.eeee...eeeeee..ee........eeeee....eeeee........eeeeeeeee..eeeeeeeeeee.......eeeeeeee....eeeeee.........eeeeeeeeee......eeee......eeee.......eeeeeeeeee..........eeee...........eeeeee...eeeeee...........eeeeeee.-----.....ee.....eeee.......eeeeeeeeee..ee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------P--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FN3  PDB: A:498-591 UniProt: 498-591                                                          -FN3  PDB: A:593-688 UniProt: 593-688                                                            - PROSITE
           Transcript 1 (1) Exon 1.13b  PDB: A:301-348 (gaps) [INCOMPLETE]  Exon 1.14b  PDB: A:349-399 UniProt: 349-399        --------------------------------------------------------------Exon 1.16  PDB: A:462-494        ---------------------------------------------------------Exon 1.19  PDB: A:552-592                ----------------------------------------Exon 1.21  PDB: A:638-689 UniProt: 633-693 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------Exon 1.15  PDB: A:399-461 UniProt: 399-461                     --------------------------------Exon 1.17  PDB: A:494-552 UniProt: 494-552                 ---------------------------------------Exon 1.20  PDB: A:592-632                --------------------------------------------------------- Transcript 1 (2)
                 2jll A 301 QPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDGFTFTE--KSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISNQTIYYSWEGNPINISCDVKSNPPASIHWRRDKLVLPAKNTTNLKTYSTGRKMILEIAPTSDNDFGRYNCTATNHIGTRFQEYILALADVPSSPYGVKIIELSQTTAKVSFNKPDSHGGVPIHHYQVDVKEVASEIWKIVRSHGVQTMVVLNNLEPNTTYEIRVAAVNGKGQGDYSKIEIFQTLPVREPSPPSIHGQPSSGKSFKLSITKQDDGGAPILEYIVKYRS-----QWLEKKVQGNKDHIILEHLQWTMGYEVQITAANRLGYSEPTVYEFSMPPKPN 689
                                   310       320       330       340    |  350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630 |     640       650       660       670       680         
                                                                      345  |                                                                                                                                                                                                                                                                                         632   638                                                   
                                                                         348

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 2JLL)

Asymmetric/Biological 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)

2jllA04

A:593-689

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: fn3 (66)

Homo sapiens (Human) (52)

1a	fn3-2jllA01	A:593-678
1b	fn3-2jllA02	A:593-678

Clan: Ig (577)

Family: I-set (67)

Homo sapiens (Human) (50)

2a	I-set-2jllA03	A:401-492
2b	I-set-2jllA04	A:401-492

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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/Biological Unit
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	Cis Peptide Bonds
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		Glu A:327 - Pro A:328	[ RasMol ]
		Leu A:441 - Pro A:442	[ RasMol ]
		Lys A:348 - Ser A:349	[ RasMol ]
		Ser A:605 - Gly A:606	[ RasMol ]

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

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 2)

Exons (8, 8)

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