1NT0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CUB1-EGF-CUB2 REGION OF MASP2

Authors :   H. Feinberg, J. C. M. Uitdehaag, J. M. Davies, R. Wallis, K. Drickamer, W

Date :   28 Jan 03 (Deposition) - 20 May 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,G

Keywords :   Mannose-Binding Protein, Masp, Cub Domain, Egf Like Domain. , Hydrolase, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Feinberg, J. C. M. Uitdehaag, J. M. Davies, R. Wallis, K. Drickamer, W. I. Weis
Crystal Structure Of The Cub1-Egf-Cub2 Region Of Mannose-Binding Protein Associated Serine Protease-2
Embo J. V. 22 2348 2003
PubMed-ID: 12743029 | Reference-DOI: 10.1093/EMBOJ/CDG236

Molecule 1 - MANNOSE-BINDING PROTEIN ASSOCIATED SERINE PROTEASE-2
	Chains	:	A, G
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Expression System Tissue	:	OVARY CELLS
	Fragment	:	CUB1-EGF-CUB2
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	MASP2

		1	2
Asymmetric/Biological Unit	:	A	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	AHB	2	Mod. Amino Acid	BETA-HYDROXYASPARAGINE
2	CA	2	Ligand/Ion	CALCIUM ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:83 , ASN A:84	BINDING SITE FOR RESIDUE NAG A 1001
2	AC2	SOFTWARE	GLY G:83 , ASN G:84	BINDING SITE FOR RESIDUE NAG G 2001
3	AC3	SOFTWARE	ASP A:119 , VAL A:120 , AHB A:139 , TYR A:140 , GLY A:143 , HOH A:8033	BINDING SITE FOR RESIDUE CA A 3001
4	AC4	SOFTWARE	ASP G:119 , VAL G:120 , AHB G:139 , TYR G:140 , GLY G:143 , HOH G:9033	BINDING SITE FOR RESIDUE CA G 4001
5	AC5	SOFTWARE	VAL A:12 , SER A:13 , GLY A:15 , ARG A:26	BINDING SITE FOR RESIDUE EDO A 5001
6	AC6	SOFTWARE	VAL G:12 , SER G:13 , GLY G:15 , ARG G:26	BINDING SITE FOR RESIDUE EDO G 6001

Asymmetric/Biological Unit

No.	Residues
1	A:53	-	A:71
2	A:123	-	A:137
3	A:133	-	A:146
4	A:148	-	A:161
5	A:165	-	A:192
6	A:222	-	A:240
7	G:53	-	G:71
8	G:123	-	G:137
9	G:133	-	G:146
10	G:148	-	G:161
11	G:165	-	G:192
12	G:222	-	G:240

Asymmetric/Biological Unit

No.	Residues
1	Phe A:16	-	Pro A:17
2	Tyr A:182	-	Pro A:183
3	Gly A:237	-	Pro A:238
4	Phe G:16	-	Pro G:17
5	Tyr G:182	-	Pro G:183
6	Gly G:237	-	Pro G:238

(no "SAP(SNP)/Variant" information available for 1NT0)

Asymmetric/Biological Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CUB	PS01180	CUB domain profile.	MASP2_RAT	18-137 184-296	2	- A:165-277 G:165-277
2	EGF_CA	PS01187	Calcium-binding EGF-like domain signature.	MASP2_RAT	138-165	2	A:119-146 G:119-146
3	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	MASP2_RAT	156-167	2	A:137-148 G:137-148
4	EGF_2	PS01186	EGF-like domain signature 2.	MASP2_RAT	165-180	2	A:146-161 G:146-161

(no "Exon" information available for 1NT0)

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:257
 aligned with MASP2_RAT | Q9JJS8 from UniProtKB/Swiss-Prot  Length:685

    Alignment length:274
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293    
            MASP2_RAT    24 EPVFGRLVSLGFPEKYGNHQDRSWTLTAPPGFRLRLYFTHFNLELSYRCEYDFVKLTSGTKVLATLCGQESTDTERAPGNDTFYSLGPSLKVTFHSDYSNEKPFTGFEAFYAAEDVDECRTSLGDSVPCDHYCHNYLGGYYCSCRVGYILHQNKHTCSALCSGQVFTGRSGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFDVEMHPEAQCPYDSLKIQTDKREYGPFCGKTLPPRIETDSNKVTITFTTDESGNHTGWKIHYTSTA 297
               SCOP domains d1nt0a1 A:5-119 Mannose-binding protein associated serine protease 2, MASP2                                        d1nt0       a3 A:120-164                     d1nt0a2 A:165-278 Mannose-binding protein associated     s  erine protease 2, MASP2                                SCOP domains
               CATH domains 1nt0A01 A:5-119  [code=2.60.120.290, no name defined]                                                              1nt0A       02 A:120-163 Laminin            1nt0A03 A:164-278  [code=2.60.120.290, no name defined    ]                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.............eeeeee....eeeeeeeeeee...hhhhh..eeeeee..eeeeee...............eee....eeeeeee...----...eeeeeeeeee.....-------....eeeee..eeeee....eee......eee..eeeee....eeee............eeeeeee.....eeeeee.........----.--.eeeee....eeeee........ee....eeeeeee..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CUB  PDB: - UniProt: 18-137                                                                                       EGF_CA  PDB: A:119-146      ------------------CUB  PDB: A:165-277 UniProt: 184-296                                                                             - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------EGF_2           --------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nt0 A   5 EPVFGRLVSPGFPEKYGNHQDRSWTLTAPPGFRLRLYFTHFNLELSYRCEYDFVKLTSGTKVLATLCGQESTDTERAPGNDTFYSLGPSLKVTFHSDY----PFTGFEAFYAAEDVDECR-------PCDHYCHnYLGGYYCSCRVGYILHQNKHTCSALCSGQVFTGRSGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFDVEMH----C--DSLKIQTDKREYGPFCGKTLPPRIETDSNKVTITFTTDESGNHTGWKIHYTSTA 278
                                    14        24        34        44        54        64        74        84        94       | -  |    114       124       134    |  144       154       164       174       184       194       204       214  |    | -|      234       244       254       264       274    
                                                                                                                           102  107              124     132      |                                                                           217  222  |                                                     
                                                                                                                                                                139-AHB                                                                               225

Chain G from PDB  Type:PROTEIN  Length:257
 aligned with MASP2_RAT | Q9JJS8 from UniProtKB/Swiss-Prot  Length:685

    Alignment length:274
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293    
            MASP2_RAT    24 EPVFGRLVSLGFPEKYGNHQDRSWTLTAPPGFRLRLYFTHFNLELSYRCEYDFVKLTSGTKVLATLCGQESTDTERAPGNDTFYSLGPSLKVTFHSDYSNEKPFTGFEAFYAAEDVDECRTSLGDSVPCDHYCHNYLGGYYCSCRVGYILHQNKHTCSALCSGQVFTGRSGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFDVEMHPEAQCPYDSLKIQTDKREYGPFCGKTLPPRIETDSNKVTITFTTDESGNHTGWKIHYTSTA 297
               SCOP domains d1nt0g1 G:5-119 Mannose-binding protein associated serine protease 2, MASP2                                        d1nt0       g3 G:120-164                     d1nt0g2 G:165-278 Mannose-binding protein associated     s  erine protease 2, MASP2                                SCOP domains
               CATH domains 1nt0G01 G:5-119  [code=2.60.120.290, no name defined]                                                              1nt0G       02 G:120-163 Laminin            1nt0G03 G:164-278  [code=2.60.120.290, no name defined    ]                                                         CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------    ------------EGF_CA       -1nt0G05 G:119-161            ---CUB-1nt0G01 G:165-274                                                                                         ---- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------    ------------EGF_CA       -1nt0G06 G:119-161            ---CUB-1nt0G02 G:165-274                                                                                         ---- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------    ------------------       ---------------------------------CUB-1nt0G03 G:165-274                                                                                         ---- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------    ------------------       ---------------------------------CUB-1nt0G04 G:165-274                                                                                         ---- Pfam domains (4)
         Sec.struct. author ...eeeee.............eeeeee....eeeeeeeeeee...hhhhh..eeeeee..eeeeee...............eee....eeeeeee...----...eeeeeeeeee.....-------....eeeee..eeeee....eee......eee..eeeee....eeee............eeeeeee.....eeeeee.........----.--.eeeee....eeeee........ee....eeeeeee..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CUB  PDB: - UniProt: 18-137                                                                                       EGF_CA  PDB: G:119-146      ------------------CUB  PDB: G:165-277 UniProt: 184-296                                                                             - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------EGF_2           --------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nt0 G   5 EPVFGRLVSPGFPEKYGNHQDRSWTLTAPPGFRLRLYFTHFNLELSYRCEYDFVKLTSGTKVLATLCGQESTDTERAPGNDTFYSLGPSLKVTFHSDY----PFTGFEAFYAAEDVDECR-------PCDHYCHnYLGGYYCSCRVGYILHQNKHTCSALCSGQVFTGRSGFLSSPEYPQPYPKLSSCAYNIRLEEGFSITLDFVESFDVEMH----C--DSLKIQTDKREYGPFCGKTLPPRIETDSNKVTITFTTDESGNHTGWKIHYTSTA 278
                                    14        24        34        44        54        64        74        84        94       | -  |    114       124       134    |  144       154       164       174       184       194       204       214  |    | -|      234       244       254       264       274    
                                                                                                                           102  107              124     132      |                                                                           217  222  |                                                     
                                                                                                                                                                139-AHB                                                                               225

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Norway rat (Rattus norvegicus) (1)

1a	1nt0A02	A:120-163
1b	1nt0G02	G:120-163

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.290, no name defined] (10)

Norway rat (Rattus norvegicus) (1)

2a	1nt0A01	A:5-119
2b	1nt0G01	G:5-119
2c	1nt0A03	A:164-278
2d	1nt0G03	G:164-278

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CUB (11)

Family: CUB (11)

Rattus norvegicus (Rat) (1)

1a	CUB-1nt0G01	G:165-274
1b	CUB-1nt0G02	G:165-274
1c	CUB-1nt0G03	G:165-274
1d	CUB-1nt0G04	G:165-274

Clan: EGF (60)

Family: EGF_CA (18)

Rattus norvegicus (Rat) (1)

2a	EGF_CA-1nt0G05	G:119-161
2b	EGF_CA-1nt0G06	G:119-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,G (MASP2_RAT | Q9JJS8)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006956	complement activation	Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
	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: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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:237 - Pro A:238	[ RasMol ]
		Gly G:237 - Pro G:238	[ RasMol ]
		Phe A:16 - Pro A:17	[ RasMol ]
		Phe G:16 - Pro G:17	[ RasMol ]
		Tyr A:182 - Pro A:183	[ RasMol ]
		Tyr G:182 - Pro G:183	[ RasMol ]

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Description

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SS Bonds (12, 12)

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