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NMR Structure - model 1

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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   NMR STRUCTURE OF THE LCCL DOMAIN

Authors :   E. Liepinsh, M. Trexler, A. Kaikkonen, J. Weigelt, L. Banyai, L. Patthy, G. Otting

Date :   05 Jun 01 (Deposition) - 17 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Alpha-Beta Protein, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Liepinsh, M. Trexler, A. Kaikkonen, J. Weigelt, L. Banyai, L. Patthy, G. Otting
Nmr Structure Of The Lccl Domain And Implications For Dfna9 Deafness Disorder.
Embo J. V. 20 5347 2001
PubMed-ID: 11574466 | Reference-DOI: 10.1093/EMBOJ/20.19.5347
(for further references see the PDB file header)

Compounds

Molecule 1 - COCHLIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMED23
	Expression System Strain	:	JM 109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LCCL MODULE
	Gene	:	M13MP18
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	COCH-5B2

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JBI)

Sites (0, 0)

(no "Site" information available for 1JBI)

SS Bonds (2, 2)

NMR Structure

No.	Residues
1	A:8	-	A:24
2	A:28	-	A:48

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1JBI)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

NMR Structure (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_008532	P	51	S	COCH_HUMAN	Disease (DFNA9)	28938175	A	P	25	S
2	UniProt	VAR_008533	V	66	G	COCH_HUMAN	Disease (DFNA9)	121908927	A	V	40	G
3	UniProt	VAR_072249	G	87	V	COCH_HUMAN	Disease (DFNA9)	---	A	G	61	V
4	UniProt	VAR_072250	G	87	W	COCH_HUMAN	Disease (DFNA9)	---	A	G	61	W
5	UniProt	VAR_008534	G	88	E	COCH_HUMAN	Disease (DFNA9)	121908928	A	G	62	E
6	UniProt	VAR_008535	I	109	N	COCH_HUMAN	Disease (DFNA9)	121908930	A	I	83	N
7	UniProt	VAR_072251	I	109	T	COCH_HUMAN	Disease (DFNA9)	---	A	I	83	T
8	UniProt	VAR_008536	W	117	R	COCH_HUMAN	Disease (DFNA9)	121908929	A	W	91	R
9	UniProt	VAR_017175	A	119	T	COCH_HUMAN	Disease (DFNA9)	121908931	A	A	93	T

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LCCL	PS50820	LCCL domain profile.	COCH_HUMAN	28-121	1	A:2-95

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000396618	1c	ENSE00001846907	chr14:31343765-31343797	33	COCH_HUMAN	-	0	0	-	-
1.1f	ENST00000396618	1f	ENSE00002186875	chr14:31344122-31344178	57	COCH_HUMAN	1-12	12	0	-	-
1.2	ENST00000396618	2	ENSE00000654637	chr14:31344262-31344309	48	COCH_HUMAN	12-28	17	1	A:1-2	2
1.3	ENST00000396618	3	ENSE00001751450	chr14:31346778-31346934	157	COCH_HUMAN	28-80	53	1	A:2-54	53
1.4	ENST00000396618	4	ENSE00001657103	chr14:31348017-31348150	134	COCH_HUMAN	80-125	46	1	A:54-98	45
1.5	ENST00000396618	5	ENSE00001698645	chr14:31348629-31348691	63	COCH_HUMAN	125-146	22	1	A:99-100	2
1.6	ENST00000396618	6	ENSE00001610421	chr14:31349658-31349702	45	COCH_HUMAN	146-161	16	0	-	-
1.7	ENST00000396618	7	ENSE00001775943	chr14:31349793-31349940	148	COCH_HUMAN	161-210	50	0	-	-
1.8	ENST00000396618	8	ENSE00000654644	chr14:31353759-31353862	104	COCH_HUMAN	210-245	36	0	-	-
1.10	ENST00000396618	10	ENSE00000654645	chr14:31354600-31354826	227	COCH_HUMAN	245-320	76	0	-	-
1.11a	ENST00000396618	11a	ENSE00000654646	chr14:31355002-31355518	517	COCH_HUMAN	321-493	173	0	-	-
1.12d	ENST00000396618	12d	ENSE00001953870	chr14:31358822-31359824	1003	COCH_HUMAN	493-550	58	0	-	-

Sequences/Alignments

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:100
 aligned with COCH_HUMAN | O43405 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
           COCH_HUMAN    27 AAPIAITCFTRGLDIRKEKADVLCPGGCPLEEFSVYGNIVYASVSSICGAAVHRGVISNSGGPVRVYSLPGRENYSSVDANGIQSQMLSRWSASFTVTKGKSSTQE 132
               SCOP domains d1jbia_ A: Cochlin                                                                                         SCOP domains
               CATH domains 1jbiA00 A:1-100  [code=2.170.130.20, no name defined]                                                      CATH domains
               Pfam domains -----LCCL-1jbiA01 A:6-95                                                                       ----------- Pfam domains
         Sec.struct. author ...ee.............eeeeee..........ee....ee...hhhhhhhhhh......eeeeeeee........ee....eee.......eeeee------.. Sec.struct. author
             SAPs(SNPs) (1) ------------------------S--------------G--------------------VE--------------------N-------R-T------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------W---------------------T----------------------- SAPs(SNPs) (2)
                    PROSITE -LCCL  PDB: A:2-95 UniProt: 28-121                                                             ----------- PROSITE
           Transcript 1 (1) 1.---------------------------------------------------Exon 1.4  PDB: A:54-98 UniProt: 80-125        ------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: A:2-54 UniProt: 28-80                 --------------------------------------------Exon 1.5 Transcript 1 (2)
                 1jbi A   1 TAPIAITCFTRGLDIRKEKADVLCPGGCPLEEFSVYGNIVYASVSSICGAAVHRGVISNSGGPVRVYSLPGRENYSSVDANGIQSQMLSRWSASFTVT------LE 100
                                    10        20        30        40        50        60        70        80        90       | -    | 
                                                                                                                            98     99

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, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: LCCL domain (1)

Superfamily: LCCL domain (1)

Family: LCCL domain (1)

Protein domain: Cochlin (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1jbia_

CATH Domains (1, 1)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Ferric Hydroxamate Uptake Protein; Chain A, domain 1 (37)

Homologous Superfamily: [code=2.170.130.20, no name defined] (1)

Human (Homo sapiens) (1)

1jbiA00

A:1-100

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LCCL-domain (1)

Family: LCCL (1)

Homo sapiens (Human) (1)

LCCL-1jbiA01

A:6-95

Gene Ontology (10, 10)

NMR Structure(hide GO term definitions)

Chain A (COCH_HUMAN | O43405)

molecular function
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	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:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045089	positive regulation of innate immune response	Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0007605	sensory perception of sound	The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
cellular component
	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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (1, 1)

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