2E3V - JenaLib

Title :   CRYSTAL STRUCTURE OF THE FIRST FIBRONECTIN TYPE III DOMAIN OF NEURAL CELL ADHESION MOLECULE SPLICING ISOFORM FROM HUMAN MUSCLE CULTURE LAMBDA-4.4

Authors :   A. Nishino, S. Saijo, S. Kishishita, L. Chen, Z. J. Liu, B. C. Wang, M. Shi S. Yokoyama, Riken Structural Genomics/Proteomics Initiative

Date :   30 Nov 06 (Deposition) - 05 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Ncam, N-Cam 1, Ncam-120, Cd56 Antigen, Cell Adhesion, Membrane Protein, Glycoprotein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Saijo, A. Nishino, S. Kishishita, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yokoyama
Crystal Structure Of The First Fibronectin Type Iii Domain Of Neural Cell Adhesion Molecule Splicing Isoform From Huma Muscle Culture Lambda-4. 4
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 3 (4, 4)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE C:40 , ALA C:62 , LYS C:63 , SER C:66	BINDING SITE FOR RESIDUE EDO C 1001
2	AC2	SOFTWARE	VAL A:50 , HOH A:1092 , ARG B:48 , TYR B:82 , ALA B:83 , ALA B:100 , GLU B:102 , HOH B:1038	BINDING SITE FOR RESIDUE PGE B 1006
3	AC3	SOFTWARE	ALA A:100 , GLU A:102 , ALA B:49 , VAL B:50 , GLY B:51 , LYS B:77 , THR B:80 , HOH B:1060	BINDING SITE FOR RESIDUE PGE B 1007
4	AC4	SOFTWARE	LYS A:58 , HOH A:1090 , PHE C:29 , GLU C:31 , PRO C:32 , GLU C:33 , ALA C:34 , ILE C:40 , TYR C:43 , SER C:66 , GLY C:69 , HOH C:1061	BINDING SITE FOR RESIDUE BTB C 1008
5	AC5	SOFTWARE	GLN A:17 , GLU A:19 , GLN A:28 , LYS B:44 , GLU B:46 , TRP B:55 , SER B:57 , HOH B:1093	BINDING SITE FOR RESIDUE BTB B 1009
6	AC6	SOFTWARE	GLY A:75 , LYS C:63 , GLU C:64 , SER C:66 , MSE C:67	BINDING SITE FOR RESIDUE PEG C 1003
7	AC7	SOFTWARE	PHE A:29 , ASP A:30 , GLU A:31 , PRO A:32 , GLU A:33 , TYR A:43 , GLY A:69 , HOH A:1049 , LYS B:58 , HOH B:1030	BINDING SITE FOR RESIDUE PEG A 1004
8	AC8	SOFTWARE	HOH A:1093 , LEU B:41 , LYS B:42 , ASN B:90 , HOH B:1090	BINDING SITE FOR RESIDUE PEG B 1005

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (3, 7)

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:103
 aligned with NCAM1_HUMAN | P13591 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:106
                                   517       527       537       547       557       567       577       587       597       607      
          NCAM1_HUMAN   508 DTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPVQGEPS 613
               SCOP domains d2e3va_ A: Neural cell adhes  ion molecule 1, NCAM                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....eeeeee.....--..eeeeeeeeee......eeeeeehhhhhh..eeee.......eeeeeeeeee..ee......eeee.....-... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FN3  PDB: A:10-108 UniProt: 509-608                                                                 --FN3 PROSITE
           Transcript 1 (1) Exon 1.19b  PDB: A:8-64 (gaps) UniProt: 507-564          --------------------------------------------1.28c Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.20b  PDB: A:64-109 UniProt: 564-609    ---- Transcript 1 (2)
                 2e3v A   8 SGPSSPSIDQVEPYSSTAQVQFDEPEAT--VPILKYKAEWRAVGEEVWHSKWYDAKEASmEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPVR-EPS 112
                                    17        27       | -|       47        57        67        77        87        97       107 | |  
                                                      35 38                           67-MSE                                   109 |  
                                                                                                                                 110

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with NCAM1_HUMAN | P13591 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:101
                                   517       527       537       547       557       567       577       587       597       607 
          NCAM1_HUMAN   508 DTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPV 608
               SCOP domains d2e3vb_ B: Neural cell adh    esion molecule 1, NCAM                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....eeeeee...----....eeeeeeee......eeeeeehhhhhh..eeee.......eeeeeeeeee..ee......eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FN3  PDB: B:10-108 UniProt: 509-608                                                                  PROSITE
           Transcript 1 (1) Exon 1.19b  PDB: B:8-64 (gaps) UniProt: 507-564          -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.20b  PDB: B:64-108 UniProt: 564-609    Transcript 1 (2)
                 2e3v B   8 SGPSSPSIDQVEPYSSTAQVQFDEPE----VPILKYKAEWRAVGEEVWHSKWYDAKEASmEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPV 108
                                    17        27     |   -|       47        57        67        77        87        97       107 
                                                    33   38                           67-MSE

Chain C from PDB  Type:PROTEIN  Length:101
 aligned with NCAM1_HUMAN | P13591 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:101
                                   517       527       537       547       557       567       577       587       597       607 
          NCAM1_HUMAN   508 DTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPV 608
               SCOP domains d2e3vc_ C: Neural cell adhesion molecule 1, NCAM                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...eeeeeee...........eeeeeeee......eeeeeehhhhhh..eeeee......eeeeeeeeee..ee......eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FN3  PDB: C:10-108 UniProt: 509-608                                                                  PROSITE
           Transcript 1 (1) Exon 1.19b  PDB: C:8-64 UniProt: 507-564 [INCOMPLETE]    -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.20b  PDB: C:64-108 UniProt: 564-609    Transcript 1 (2)
                 2e3v C   8 SGPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASmEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPV 108
                                    17        27        37        47        57        67        77        87        97       107 
                                                                                      67-MSE

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 (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (22, 22)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NCAM1_HUMAN | P13591)

molecular function
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	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:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0031175	neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0048167	regulation of synaptic plasticity	A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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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