2KA3 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURE OF EMILIN-1 C1Q-LIKE DOMAIN

Authors :   G. Verdone, A. Corazza, S. A. Colebrooke, D. O. Cicero, T. Eliseo, J. Boyd, R. Doliana, F. Fogolari, P. Viglino, A. Colombatti, I. D. Campbell, G. Esposito

Date :   30 Oct 08 (Deposition) - 25 Nov 08 (Release) - 09 Jun 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (10x)

Keywords :   Emilin-1, C1Q-Like Domain, Homotrimeric Protein Complex, Beta-Sandwich, Structural Protein, Cell Adhesion, Extracellular Matrix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Verdone, A. Corazza, S. A. Colebrooke, D. Cicero, T. Eliseo, J. Boyd, R. Doliana, F. Fogolari, P. Viglino, A. Colombatti, I. D. Campbell, G. Esposito
Nmr-Based Homology Model For The Solution Structure Of The C-Terminal Globular Domain Of Emilin1
J. Biomol. Nmr V. 43 79 2009
PubMed-ID: 19023665 | Reference-DOI: 10.1007/S10858-008-9290-Y
(for further references see the PDB file header)

Molecule 1 - EMILIN-1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-30
	Expression System Taxid	:	562
	Expression System Variant	:	M15 CELLS
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, C1Q DOMAIN, UNP RESIDUES 867- 1016
	Gene	:	EM1, EMILIN1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ELASTIN MICROFIBRIL INTERFACE-LOCATED PROTEIN 1, ELASTIN MICROFIBRIL INTERFACER 1


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KA3)

(no "Site" information available for 2KA3)

(no "SS Bond" information available for 2KA3)

(no "Cis Peptide Bond" information available for 2KA3)

NMR Structure (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046097	E	903	K	EMIL1_HUMAN	Polymorphism	36045790	A/B/C	E	882	K

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

(no "PROSITE Motif" information available for 2KA3)

NMR Structure (2, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000380320	1	ENSE00001484569	chr2:27301435-27302103	669	EMIL1_HUMAN	1-57	57	0	-	-
1.2	ENST00000380320	2	ENSE00000732220	chr2:27303019-27303138	120	EMIL1_HUMAN	57-97	41	0	-	-
1.3	ENST00000380320	3	ENSE00000732221	chr2:27303600-27303820	221	EMIL1_HUMAN	97-171	75	0	-	-
1.4a	ENST00000380320	4a	ENSE00000809129	chr2:27304951-27306879	1929	EMIL1_HUMAN	171-814	644	0	-	-
1.5	ENST00000380320	5	ENSE00000732225	chr2:27307283-27307399	117	EMIL1_HUMAN	814-853	40	0	-	-
1.6	ENST00000380320	6	ENSE00001802271	chr2:27307859-27307876	18	EMIL1_HUMAN	853-859	7	0	-	-
1.7	ENST00000380320	7	ENSE00000809130	chr2:27308028-27308165	138	EMIL1_HUMAN	859-905	47	3	A:846-884 B:846-884 C:846-884	39 39 39
1.8	ENST00000380320	8	ENSE00001669474	chr2:27308546-27309271	726	EMIL1_HUMAN	905-1016	112	3	A:884-995 (gaps) B:884-995 (gaps) C:884-995 (gaps)	112 112 112

NMR Structure

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:131
 aligned with EMIL1_HUMAN | Q9Y6C2 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:150
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016
         EMIL1_HUMAN    867 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGGYEPEGLENKPVAESQPSPGTLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA 1016
               SCOP domains d2ka3a_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..............eeeee....ee....eee....eeeeeee.........eeeee..........eee.-------------------...............eeeee...............eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------K----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:846-884 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8  PDB: A:884-995 (gaps) UniProt: 905-1016                                                                Transcript 1 (2)
                2ka3 A  846 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGG-------------------TLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA  995
                                   855       865       875       885       895       905       915       925|        -         -|      955       965       975       985       995
                                                                                                          926                 946

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with EMIL1_HUMAN | Q9Y6C2 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:150
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016
         EMIL1_HUMAN    867 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGGYEPEGLENKPVAESQPSPGTLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA 1016
               SCOP domains d2ka3b_ B: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..............eeeee....ee....eee....eeeeeee.........eeeee..........eee.-------------------...............eeeee...............eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------K----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7  PDB: B:846-884 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8  PDB: B:884-995 (gaps) UniProt: 905-1016                                                                Transcript 1 (2)
                2ka3 B  846 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGG-------------------TLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA  995
                                   855       865       875       885       895       905       915       925|        -         -|      955       965       975       985       995
                                                                                                          926                 946

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with EMIL1_HUMAN | Q9Y6C2 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:150
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016
         EMIL1_HUMAN    867 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGGYEPEGLENKPVAESQPSPGTLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA 1016
               SCOP domains d2ka3c_ C: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----C1q-2ka3C01 C:851-986                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) -----C1q-2ka3C02 C:851-986                                                                                                                   --------- Pfam domains (2)
           Pfam domains (3) -----C1q-2ka3C03 C:851-986                                                                                                                   --------- Pfam domains (3)
         Sec.struct. author .....eeeee..............eeeee....ee....eee....eeeeeee.........eeeee..........eee.-------------------...............eeeee...............eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------K----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7  PDB: C:846-884 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8  PDB: C:884-995 (gaps) UniProt: 905-1016                                                                Transcript 1 (2)
                2ka3 C  846 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGG-------------------TLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA  995
                                   855       865       875       885       895       905       915       925|        -         -|      955       965       975       985       995
                                                                                                          926                 946

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: TNF-like (100)

Superfamily: TNF-like (100)

Family: automated matches (18)

Protein domain: automated matches (18)

Human (Homo sapiens) [TaxId: 9606] (18)

1a	d2ka3a_	A:
1b	d2ka3b_	B:
1c	d2ka3c_	C:

(no "CATH Domain" information available for 2KA3)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C1q_TNF (45)

Family: C1q (8)

Homo sapiens (Human) (7)

1a	C1q-2ka3C01	C:851-986
1b	C1q-2ka3C02	C:851-986
1c	C1q-2ka3C03	C:851-986

NMR Structure(hide GO term definitions)

Chain A,B,C (EMIL1_HUMAN | Q9Y6C2)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
cellular component
	GO:0005581	collagen trimer	A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
	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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

NMR Structure
	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 2ka3)

	Sites
(no "Sites" information available for 2ka3)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ka3)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models 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)

Access by PDB/NDB ID
	2ka3
		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
	EMIL1_HUMAN \| Q9Y6C2
		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

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
	EMIL1_HUMAN \| Q9Y6C2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	EMIL1_HUMAN \| Q9Y6C2	:	2oii

1c28	ACRP-30 CHAIN A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

PROSITE Motifs (0, 0)

Exons (2, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File