2FMW - JenaLib

Theor.Model - manually

Theoretical Model

collapse

expand

Theor.Model - manually (Jmol Viewer)

Theoretical Model (Jmol Viewer)

Description

Title :   A MODEL OF THE EGF DOMAIN FOR TMEFF1

Authors :   W. -T. Ge, H. -G. Hu, K. -F. Ding, L. -F. Sun, S. Zheng

Date :   10 Jan 06 (Deposition) - 31 Jan 06 (Release) - 31 Jan 06 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Egf Domain, Modeling, Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. -T. Ge, H. -G. Hu, K. -F. Ding, L. -F. Sun, S. Zheng
Protein Interaction Analysis Of St14 Domains And Their Point And Deletion Mutants
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - TRANSMEMBRANE PROTEIN WITH EGF-LIKE AND TWO FOLLISTATIN-LIKE DOMAINS 2
	Chains	:	A
	Fragment	:	EGF DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	TMEFF1, TRANSMEMBRANE PROTEIN CONTAINING EPIDERMAL GROWTH FACTOR AND FOLLISTATIN DOMAINS, TOMOREGULIN, TR, HYPERPLASTIC POLYPOSIS PROTEIN 1

Structural Features

Chains, Units


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2FMW)

SS Bonds (3, 3)

Theoretical Model

No.	Residues
1	A:3	-	A:16
2	A:11	-	A:27
3	A:29	-	A:38

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (2, 1)

Theoretical Model (2, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_1	PS00022	EGF-like domain signature 1.	TEFF2_HUMAN	289-300	1	A:27-38
2	EGF_2	PS01186	EGF-like domain signature 2.	TEFF2_HUMAN	289-300	1	A:27-38

Exons (2, 2)

Theoretical Model (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000272771	1a	ENSE00001511404	chr2:193060435-193059079	1357	TEFF2_HUMAN	1-58	58	0	-	-
1.2	ENST00000272771	2	ENSE00000964661	chr2:193056715-193056606	110	TEFF2_HUMAN	58-94	37	0	-	-
1.3	ENST00000272771	3	ENSE00000964662	chr2:193049209-193049080	130	TEFF2_HUMAN	95-138	44	0	-	-
1.4a	ENST00000272771	4a	ENSE00001182100	chr2:193044420-193044394	27	TEFF2_HUMAN	138-147	10	0	-	-
1.5	ENST00000272771	5	ENSE00001165586	chr2:192922501-192922405	97	TEFF2_HUMAN	147-179	33	0	-	-
1.6a	ENST00000272771	6a	ENSE00001182093	chr2:192863934-192863786	149	TEFF2_HUMAN	179-229	51	0	-	-
1.7	ENST00000272771	7	ENSE00001128682	chr2:192863047-192862988	60	TEFF2_HUMAN	229-249	21	0	-	-
1.9	ENST00000272771	9	ENSE00001128675	chr2:192821104-192820981	124	TEFF2_HUMAN	249-290	42	1	A:2-28	27
1.10	ENST00000272771	10	ENSE00001152395	chr2:192818563-192818405	159	TEFF2_HUMAN	290-343	54	1	A:28-39	12
1.11b	ENST00000272771	11b	ENSE00001253916	chr2:192815133-192814743	391	TEFF2_HUMAN	343-374	32	0	-	-

Sequences/Alignments

Theoretical Model

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:38
 aligned with TEFF2_HUMAN | Q9UIK5 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:38
                                   273       283       293        
          TEFF2_HUMAN   264 PCPEHYNGFCMHGKCEHSINMQEPSCRCDAGYTGQHCE 301
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ............eee..........eee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------EGF_1       - PROSITE (1)
                PROSITE (2) -------------------------EGF_2       - PROSITE (2)
           Transcript 1 (1) --------------------------Exon 1.10    Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:2-28      ----------- Transcript 1 (2)
                 2fmw A   2 PCPEHYNGFCMHGKCEHSINMQEPSCRCDAGYTGQHCE  39
                                    11        21        31

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 2FMW)

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2FMW)

Gene Ontology (8, 8)

Theoretical Model(hide GO term definitions)

Chain A (TEFF2_HUMAN | Q9UIK5)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0045720	negative regulation of integrin biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins.
	GO:0051497	negative regulation of stress fiber assembly	Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	GO:0044319	wound healing, spreading of cells	The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface.
cellular component
	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.

Visualization

Interactive Views

Theoretical Model
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

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

	Sites
(no "Sites" information available for 2fmw)

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

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Theoretical Model PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2fmw
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TEFF2_HUMAN \| Q9UIK5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TEFF2_HUMAN \| Q9UIK5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)