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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE N-TERMINAL FOUR DOMAINS OF THE COMPLEMENT REGULATOR RAT CRRY

Authors :   K. J. Leath, P. Roversi, S. Johnson, B. P. Morgan, S. M. Lea

Date :   14 Sep 10 (Deposition) - 22 Jun 11 (Release) - 19 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

Chains :   Asym./Biol. Unit : A

Keywords :   Immune System, Extracellular Protein, Sushi (Ccp/Scr) Domains (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Roversi, S. Johnson, J. J. E. Caesar, F. Mclean, K. J. Leath, S. A. Tsiftsoglou, B. P. Morgan, C. L. Harris, R. B. Sim, S. M. Lea
Structures Of The Rat Complement Regulator Crry.
Acta Crystallogr. , Sect. F V. 67 739 2011
PubMed-ID: 21795784 | Reference-DOI: 10.1107/S1744309111016551

Molecule 1 - COMPLEMENT REGULATORY PROTEIN CRRY
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET SERIES
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR N-TERMINAL FOUR CCP DOMAINS, RESIDUES 1-288
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CRRY, ANTIGEN 5I2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2XRD)

Asymmetric/Biological Unit

No.	Residues
1	A:38	-	A:81
2	A:68	-	A:94
3	A:99	-	A:140
4	A:126	-	A:156
5	A:161	-	A:210
6	A:190	-	A:227
7	A:233	-	A:275
8	A:261	-	A:288

Asymmetric/Biological Unit

No.	Residues
1	Glu A:282	-	Pro A:283

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

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUSHI	PS50923	Sushi/CCP/SCR domain profile.	CR1L_RAT	36-96 97-158 159-229 231-290 292-354 355-415 417-477	3	- A:97-158 A:159-229 A:231-288 - - -

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000010799	1	ENSRNOE00000344752	chr13:111057427-111057067	361	CR1L_RAT	1-36	36	0	-	-
1.2	ENSRNOT00000010799	2	ENSRNOE00000259154	chr13:111054088-111053909	180	CR1L_RAT	36-96	61	1	A:37-96 (gaps)	60
1.3	ENSRNOT00000010799	3	ENSRNOE00000259145	chr13:111053179-111053080	100	CR1L_RAT	96-129	34	1	A:96-129	34
1.4	ENSRNOT00000010799	4	ENSRNOE00000258717	chr13:111047369-111047284	86	CR1L_RAT	129-158	30	1	A:129-158	30
1.5	ENSRNOT00000010799	5	ENSRNOE00000258708	chr13:111032883-111032485	399	CR1L_RAT	158-291	134	1	A:158-289 (gaps)	132
1.6	ENSRNOT00000010799	6	ENSRNOE00000258698	chr13:111029696-111029594	103	CR1L_RAT	291-325	35	0	-	-
1.7	ENSRNOT00000010799	7	ENSRNOE00000258691	chr13:111028340-111028255	86	CR1L_RAT	325-354	30	0	-	-
1.8	ENSRNOT00000010799	8	ENSRNOE00000258677	chr13:111025811-111025626	186	CR1L_RAT	354-416	63	0	-	-
1.9	ENSRNOT00000010799	9	ENSRNOE00000362867	chr13:111021835-111021650	186	CR1L_RAT	416-478	63	0	-	-
1.10	ENSRNOT00000010799	10	ENSRNOE00000258669	chr13:111019296-111019273	24	CR1L_RAT	478-486	9	0	-	-
1.11	ENSRNOT00000010799	11	ENSRNOE00000258661	chr13:111018067-111017992	76	CR1L_RAT	486-511	26	0	-	-
1.12	ENSRNOT00000010799	12	ENSRNOE00000281590	chr13:111013671-111013567	105	CR1L_RAT	511-546	36	0	-	-
1.13	ENSRNOT00000010799	13	ENSRNOE00000076758	chr13:111010497-111010302	196	CR1L_RAT	546-559	14	0	-	-

Asymmetric/Biological 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:248
 aligned with CR1L_RAT | Q63135 from UniProtKB/Swiss-Prot  Length:559

    Alignment length:253
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286   
             CR1L_RAT    37 QCPAPPLFPYAKPINPTDESTFPVGTSLKYECRPGYIKRQFSITCEVNSVWTSPQDVCIRKQCETPLDPQNGIVHVNTDIRFGSSITYTCNEGYRLIGSSSAMCIISDQSVAWDAEAPICESIPCEIPPSIPNGDFFSPNREDFHYGMVVTYQCNTDARGKKLFNLVGEPSIHCTSIDGQVGVWSGPPPQCIELNKCTPPHVENAVIVSKNKSLFSLRDMVEFRCQDGFMMKGDSSVYCRSLNRWEPQLPSCF 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee...-.........eeeeee.......eeeeee.....ee...................eeeee........eeeeee...eeee...eeeeeee..eeee.....eeee.ee........eeee..---.ee...eeeeee.........eeee...eeeeee.....eee.....eeee..ee.......eee.......ee...eeeeee.....ee...eeeee...eee..-.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SUSHI  PDB: - UniProt: 36-96                                SUSHI  PDB: A:97-158 UniProt: 97-158                          SUSHI  PDB: A:159-229 UniProt: 159-229                                 -SUSHI  PDB: A:231-288 UniProt: 231-290                      PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:37-96 (gaps) UniProt: 36-96 [INCOMPLETE]   --------------------------------Exon 1.4  PDB: A:129-158      ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.3  PDB: A:96-129           ----------------------------Exon 1.5  PDB: A:158-289 (gaps) UniProt: 158-291 [INCOMPLETE]                                                                        Transcript 1 (2)
                 2xrd A  37 QCPAPPLFPYAKPINP-DESTFPVGTSLKYECRPGYIKRQFSITCEVNSVWTSPQDVCIRKQCETPLDPQNGIVHVNTDIRFGSSITYTCNEGYRLIGSSSAMCIISDQSVAWDAEAPICESIPCEIPPSIPNGDFFSP---DFHYGMVVTYQCNTDARGKKLFNLVGEPSIHCTSIDGQVGVWSGPPPQCIELNKCTPPHVENAVIVSKNKSLFSLRDMVEFRCQDGFMMKGDSSVYCRSLNRWEPQ-PSCA 289
                                    46     | |56        66        76        86        96       106       116       126       136       146       156       166        |-  |    186       196       206       216       226       236       246       256       266       276       286   
                                          52 |                                                                                                                      175 179                                                                                                      284 |   
                                            54                                                                                                                                                                                                                                     286

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 '\|'

(no "SCOP Domain" information available for 2XRD)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CR1L_RAT | Q63135)

biological process
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0045916	negative regulation of complement activation	Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation.
cellular component
	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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2xrd)

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

	Cis Peptide Bonds
		Glu A:282 - Pro A:283	[ RasMol ]

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Access by PDB/NDB ID
	2xrd
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	CR1L_RAT \| Q63135
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	CR1L_RAT \| Q63135
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UniProtKB/Swiss-Prot
	CR1L_RAT \| Q63135	:	1ntj 2xrb

1ntj	MODEL OF RAT CRRY DETERMINED BY SOLUTION SCATTERING, CURVEFITTING AND HOMOLOGY MODELLING
2xrb	STRUCTURE OF THE N-TERMINAL FOUR DOMAINS OF THE COMPLEMENT REGULATOR RAT CRRY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (8, 8)

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