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Asymmetric Unit

Biological Unit 1

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Biological Unit 1 (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF NCAM2 IG1 (I4122 CELL UNIT)

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

Date :   31 Aug 07 (Deposition) - 26 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

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

Reference :   K. K. Rasmussen, N. Kulahin, O. Kristensen, J. C. Poulsen, B. W. Sigurskjold, J. S. Kastrup, V. Berezin, E. Bock, P. S. Walmod, M. Gajhede
Crystal Structure Of The Ig1 Domain Of The Neural Cell Adhesion Molecule Ncam2 Displays Domain Swapping.
J. Mol. Biol. V. 382 1113 2008
PubMed-ID: 18706912 | Reference-DOI: 10.1016/J.JMB.2008.07.084

Compounds

Molecule 1 - NEURAL CELL ADHESION MOLECULE 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	PROCHLOROCOCCUS MARINUS SUBSP. PASTORIS
	Expression System Cell Line	:	KM71H
	Expression System Taxid	:	142479
	Expression System Vector	:	PPICZALFAC
	Fragment	:	IG1, RESIDUES 21-113
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NCAM2, N-CAM 2

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2VAJ)

Sites (0, 0)

(no "Site" information available for 2VAJ)

SS Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	A:22	-	A:73

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

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

Exons (3, 3)

Asymmetric Unit (3, 3)

	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	1	A:1-24	24
1.7	ENST00000400546	7	ENSE00001017039	chr21:22656514-22656720	207	NCAM2_HUMAN	44-113	70	1	A:24-93	70
1.8	ENST00000400546	8	ENSE00001017049	chr21:22658589-22658732	144	NCAM2_HUMAN	113-161	49	1	A:93-93	1
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	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	-	-

Sequences/Alignments

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:93
 aligned with NCAM2_HUMAN | O15394 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:93
                                    30        40        50        60        70        80        90       100       110   
          NCAM2_HUMAN    21 LQVTISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNANIEDAGIYRCQATDAKGQTQEATVVLEIYQ 113
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vajA00 A:1-93 Immunoglobulins                                                                CATH domains
               Pfam domains I-set-2vajA01 A:1-91                                                                       -- Pfam domains
         Sec.struct. author ........eeeee....eeeeee......eeeee............eeeeee..eeeeee...hhhhheeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:1-24   --------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.7  PDB: A:24-93 UniProt: 44-113                                 Transcript 1 (2)
                 2vaj A   1 LQVTISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNANIEDAGIYRCQATDAKGQTQEATVVLEIYQ  93
                                    10        20        30        40        50        60        70        80        90

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 2VAJ)

CATH Domains (1, 1)

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)

2vajA00

A:1-93

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: I-set (67)

Homo sapiens (Human) (50)

I-set-2vajA01

A:1-91

Gene Ontology (6, 6)

Asymmetric 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.

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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 2vaj)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vaj)

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	2vaj
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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

Related Entries Specified in the PDB File

2doc	SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE- III DOMAIN OFHUMAN NEURAL CELL ADHESION MOLECULE 2
2v44	CRYSTAL STRUCTURE OF NCAM2 IG1-2
2v5t	CRYSTAL STRUCTURE OF NCAM2 IG2-3
2va4	CRYSTAL STRUCTURE OF NCAM2 IG34