1GR3 - JenaLib

Title :   STRUCTURE OF THE HUMAN COLLAGEN X NC1 TRIMER

Authors :   O. Bogin, M. Kvansakul, E. Rom, J. Singer, A. Yayon, E. Hohenester

Date :   12 Dec 01 (Deposition) - 14 Feb 02 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Collagen, Extracellular Matrix, Connective Tissue (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Bogin, M. Kvansakul, E. Rom, J. Singer, A. Yayon, E. Hohenester
Insight Into Schmid Metaphyseal Chondrodysplasia From The Crystal Structure Of The Collagen X Nc1 Domain Trimer.
Structure V. 10 165 2002
PubMed-ID: 11839302 | Reference-DOI: 10.1016/S0969-2126(02)00697-4
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (17, 17)

Asymmetric Unit (17, 17)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_023188	Y	582	D	COAA1_HUMAN	Disease (SMCD)	---	A	Y	582	D
02	UniProt	VAR_001841	C	591	R	COAA1_HUMAN	Disease (SMCD)	111033546	A	C	591	R
03	UniProt	VAR_001842	G	595	E	COAA1_HUMAN	Disease (SMCD)	111033553	A	G	595	E
04	UniProt	VAR_023189	G	595	R	COAA1_HUMAN	Disease (SMCD)	---	A	G	595	R
05	UniProt	VAR_008039	Y	597	C	COAA1_HUMAN	Disease (SMCD)	111033554	A	Y	597	C
06	UniProt	VAR_001843	Y	597	H	COAA1_HUMAN	Disease (SMCD)	---	A	Y	597	H
07	UniProt	VAR_001844	Y	598	D	COAA1_HUMAN	Disease (SMCD)	111033544	A	Y	598	D
08	UniProt	VAR_001845	S	600	P	COAA1_HUMAN	Disease (SMCD)	111033555	A	S	600	P
09	UniProt	VAR_023190	V	603	M	COAA1_HUMAN	Polymorphism	143769451	A	V	603	M
10	UniProt	VAR_001846	L	614	P	COAA1_HUMAN	Disease (SMCD)	111033545	A	L	614	P
11	UniProt	VAR_001847	N	617	K	COAA1_HUMAN	Disease (SMCD)	---	A	N	617	K
12	UniProt	VAR_001848	G	618	V	COAA1_HUMAN	Disease (SMCD)	---	A	G	618	V
13	UniProt	VAR_001849	L	644	R	COAA1_HUMAN	Disease (SMCD)	---	A	L	644	R
14	UniProt	VAR_001850	D	648	G	COAA1_HUMAN	Disease (SMCD)	---	A	D	648	G
15	UniProt	VAR_023191	W	651	R	COAA1_HUMAN	Disease (SMCD)	111033549	A	W	651	R
16	UniProt	VAR_023192	Q	653	P	COAA1_HUMAN	Disease (SMCD)	---	A	Q	653	P
17	UniProt	VAR_023193	S	671	P	COAA1_HUMAN	Disease (SMCD)	111033552	A	S	671	P

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

Biological Unit 1 (17, 51)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_023188	Y	582	D	COAA1_HUMAN	Disease (SMCD)	---	A	Y	582	D
02	UniProt	VAR_001841	C	591	R	COAA1_HUMAN	Disease (SMCD)	111033546	A	C	591	R
03	UniProt	VAR_001842	G	595	E	COAA1_HUMAN	Disease (SMCD)	111033553	A	G	595	E
04	UniProt	VAR_023189	G	595	R	COAA1_HUMAN	Disease (SMCD)	---	A	G	595	R
05	UniProt	VAR_008039	Y	597	C	COAA1_HUMAN	Disease (SMCD)	111033554	A	Y	597	C
06	UniProt	VAR_001843	Y	597	H	COAA1_HUMAN	Disease (SMCD)	---	A	Y	597	H
07	UniProt	VAR_001844	Y	598	D	COAA1_HUMAN	Disease (SMCD)	111033544	A	Y	598	D
08	UniProt	VAR_001845	S	600	P	COAA1_HUMAN	Disease (SMCD)	111033555	A	S	600	P
09	UniProt	VAR_023190	V	603	M	COAA1_HUMAN	Polymorphism	143769451	A	V	603	M
10	UniProt	VAR_001846	L	614	P	COAA1_HUMAN	Disease (SMCD)	111033545	A	L	614	P
11	UniProt	VAR_001847	N	617	K	COAA1_HUMAN	Disease (SMCD)	---	A	N	617	K
12	UniProt	VAR_001848	G	618	V	COAA1_HUMAN	Disease (SMCD)	---	A	G	618	V
13	UniProt	VAR_001849	L	644	R	COAA1_HUMAN	Disease (SMCD)	---	A	L	644	R
14	UniProt	VAR_001850	D	648	G	COAA1_HUMAN	Disease (SMCD)	---	A	D	648	G
15	UniProt	VAR_023191	W	651	R	COAA1_HUMAN	Disease (SMCD)	111033549	A	W	651	R
16	UniProt	VAR_023192	Q	653	P	COAA1_HUMAN	Disease (SMCD)	---	A	Q	653	P
17	UniProt	VAR_023193	S	671	P	COAA1_HUMAN	Disease (SMCD)	111033552	A	S	671	P

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

PROSITE Motifs (0, 0)

Exons (1, 1)

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:132
 aligned with COAA1_HUMAN | Q03692 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:132
                                   558       568       578       588       598       608       618       628       638       648       658       668       678  
          COAA1_HUMAN   549 MPVSAFTVILSKAYPAIGTPIPFDKILYNRQQHYDPRTGIFTCQIPGIYYFSYHVHVKGTHVWVGLYKNGTPVMYTYDEYTKGYLDQASGSAIIDLTENDQVWLQLPNAESNGLYSSEYVHSSFSGFLVAPM 680
               SCOP domains d1gr3a_ A: Collagen NC1 trimerisation domain                                                                                         SCOP domains
               CATH domains 1gr3A00 A:549-680  [code=2.60.120.40, no name defined]                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...............eeee..................eeeeeeeeeeeeeeeeeeeeee.................eeeeeeeeeee...............eeee.......eeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------D--------R---E-CD-P--M----------P--KV-------------------------R---G--R-P-----------------P--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------R-H----------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4b  PDB: A:549-680 UniProt: 52-680 [INCOMPLETE]                                                                               Transcript 1
                 1gr3 A 549 MPVSAFTVILSKAYPAIGTPIPFDKILYNRQQHYDPRTGIFTCQIPGIYYFSYHVHVKGTHVWVGLYKNGTPVMYTYDEYTKGYLDQASGSAIIDLTENDQVWLQLPNAESNGLYSSEYVHSSFSGFLVAPM 680
                                   558       568       578       588       598       608       618       628       638       648       658       668       678

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)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A (COAA1_HUMAN | Q03692)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0001958	endochondral ossification	Replacement ossification wherein bone tissue replaces cartilage.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
cellular component
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	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:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	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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