2XYC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3I

Authors :   N. Kulahin, K. K. Rasmussen, O. Kristensen, V. Berezin, E. Bock, P. S. Wa M. Gajhede

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

Method :   X-RAY DIFFRACTION

Resolution :   2.51

Chains :   Asym./Biol. Unit : A

Keywords :   Glycoprotein, Cell Adhesion (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 Taxid	:	4922
	Fragment	:	IGIV-F3I, RESIDUES 301-591
	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, 7)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:309 , TYR A:394 , HOH A:2006	BINDING SITE FOR RESIDUE NAG A1500
2	AC2	SOFTWARE	ILE A:418 , ASN A:419 , TYR A:452 , GLU A:461 , LYS A:518 , HOH A:2128	BINDING SITE FOR RESIDUE NAG A1501
3	AC3	SOFTWARE	ARG A:435 , ASP A:437 , ASN A:474 , THR A:476 , PHE A:485 , GLU A:487 , HOH A:2177 , HOH A:2178	BINDING SITE FOR RESIDUE NAG A1502
4	AC4	SOFTWARE	TYR A:411 , ALA A:493 , ASP A:494 , VAL A:495 , PRO A:496 , SER A:497 , TRP A:542 , LYS A:582 , ILE A:583 , HOH A:2157 , HOH A:2179	BINDING SITE FOR RESIDUE EPE A1503
5	AC5	SOFTWARE	GLN A:306 , LYS A:308 , ASN A:448 , SER A:466 , ASN A:468 , HOH A:2148 , HOH A:2183	BINDING SITE FOR RESIDUE PO4 A1504
6	AC6	SOFTWARE	ARG A:436 , GLY A:471 , ARG A:472 , THR A:564 , HOH A:2137 , HOH A:2175 , HOH A:2180 , HOH A:2181	BINDING SITE FOR RESIDUE PO4 A1505
7	AC7	SOFTWARE	ARG A:436 , ASP A:469 , TYR A:473 , HOH A:2182 , HOH A:2183	BINDING SITE FOR RESIDUE PO4 A1506

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

No.	Residues
1	Gln A:301	-	Pro A:302
2	Glu A:327	-	Pro A:328
3	Ile A:386	-	Gly A:387
4	Asn A:427	-	Pro A:428
5	Leu A:441	-	Pro A:442
6	Ala A:463	-	Pro A:464

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047897	D	347	N	NCAM2_HUMAN	Polymorphism	35654962	A	D	347	N
2	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, 1)

	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	1	A:498-591 -

Asymmetric/Biological Unit (6, 6)

	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	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:552-591	40
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/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
	(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:291
 aligned with NCAM2_HUMAN | O15394 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:291
                                   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 
          NCAM2_HUMAN   301 QPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISNQTIYYSWEGNPINISCDVKSNPPASIHWRRDKLVLPAKNTTNLKTYSTGRKMILEIAPTSDNDFGRYNCTATNHIGTRFQEYILALADVPSSPYGVKIIELSQTTAKVSFNKPDSHGGVPIHHYQVDVKEVASEIWKIVRSHGVQTMVVLNNLEPNTTYEIRVAAVNGKGQGDYSKIEIFQTLPV 591
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------I-set-2xycA02 A:401-492                                                                     ----fn3-2xycA01 A:497-581                                                                ---------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------I-set-2xycA03 A:401-492                                                                     --------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee...eeee....eeeeeeee.....eeeeee....eee..........eeee....eeeeee...hhhhheeeeeeee.....eeeeeeeeeeeeeee.....eeee.....eeeeeeeeee...eeeeee..ee........eeeee...eeeeee...hhhhheeeeeeeee..eeeeeeeeeee.......eeeeeeee....eeeeee...........eeeeeeee......eeee......eeee.......eeeeeeeeee..eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------N--P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FN3  PDB: A:498-591 UniProt: 498-591                                                           PROSITE
           Transcript 1 (1) Exon 1.13b  PDB: A:301-348 UniProt: 300-348     Exon 1.14b  PDB: A:349-399 UniProt: 349-399        --------------------------------------------------------------Exon 1.16  PDB: A:462-494        ---------------------------------------------------------Exon 1.19  PDB: A:552-591 [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                 --------------------------------------- Transcript 1 (2)
                 2xyc A 301 QPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISNQTIYYSWEGNPINISCDVKSNPPASIHWRRDKLVLPAKNTTNLKTYSTGRKMILEIAPTSDNDFGRYNCTATNHIGTRFQEYILALADVPSSPYGVKIIELSQTTAKVSFNKPDSHGGVPIHHYQVDVKEVASEIWKIVRSHGVQTMVVLNNLEPNTTYEIRVAAVNGKGQGDYSKIEIFQTLPV 591
                                   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

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 2XYC)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: fn3 (66)

Homo sapiens (Human) (52)

fn3-2xycA01

A:497-581

Clan: Ig (577)

Family: I-set (67)

Homo sapiens (Human) (50)

2a	I-set-2xycA02	A:401-492
2b	I-set-2xycA03	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
		Ala A:463 - Pro A:464	[ RasMol ]
		Asn A:427 - Pro A:428	[ RasMol ]
		Gln A:301 - Pro A:302	[ RasMol ]
		Glu A:327 - Pro A:328	[ RasMol ]
		Ile A:386 - Gly A:387	[ RasMol ]
		Leu A:441 - Pro A:442	[ RasMol ]

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	2xyc
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UniProtKB/Swiss-Prot
	NCAM2_HUMAN \| O15394	:	2doc 2jll 2kbg 2v5t 2vaj 2wim 2xy1 2xy2

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)
2wim	CRYSTAL STRUCTURE OF NCAM2 IG1-3
2xy1	CRYSTAL STRUCTURE OF NCAM2 IG3-4
2xy2	CRYSTAL STRUCTURE OF NCAM2 IG1-2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (6, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (2, 3)

Gene Ontology (6, 6)

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