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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN MBL-ASSOCIATED PROTEIN 19 (MAP19)

Authors :   L. A. Gregory, N. M. Thielens, G. J. Arlaud, J. C. Fontecilla-Camps, C. Gaboriaud

Date :   05 Apr 04 (Deposition) - 22 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)

Keywords :   Calcium, Complement, Innate Immunity, Cub, Egf, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. A. Gregory, N. M. Thielens, M. Matsushita, R. Sorensen, G. J. Arlaud, J. C. Fontecilla-Camps, C. Gaboriaud
The X-Ray Structure Of Human Mbl-Associated Protein 19 (Map19) And Its Interaction Site With Mannan-Binding Lectin And L-Ficolin
J. Biol. Chem. V. 279 29391 2004
PubMed-ID: 15117939 | Reference-DOI: 10.1074/JBC.M402687200
(for further references see the PDB file header)

Molecule 1 - MANNOSE BINDING LECTIN-ASSOCIATED SERINE PROTEASE-2 RELATED PROTEIN, MAP19 (19KDA)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Strain	:	HIGH FIVE INSECT CELLS
	Expression System Taxid	:	7111
	Expression System Vector	:	PBC1S
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	MASP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:123 , ILE A:124 , GLU A:126 , ASN A:143 , HIS A:144 , GLY A:147 , HOH A:1009	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	ASP B:123 , ILE B:124 , GLU B:126 , ASN B:143 , HIS B:144 , GLY B:147 , HOH B:1007	BINDING SITE FOR RESIDUE CA B 1002
3	AC3	SOFTWARE	GLU A:52 , ASP A:60 , ASP A:105 , SER A:107 , ASN A:108 , HOH A:1019	BINDING SITE FOR RESIDUE CA A 1003
4	AC4	SOFTWARE	GLU B:52 , ASP B:60 , ASP B:105 , SER B:107 , ASN B:108	BINDING SITE FOR RESIDUE CA B 1004

Asymmetric Unit

No.	Residues
1	A:57	-	A:75
2	A:127	-	A:141
3	A:137	-	A:150
4	A:152	-	A:165
5	B:57	-	B:75
6	B:127	-	B:141
7	B:137	-	B:150
8	B:152	-	B:165

Asymmetric Unit

No.	Residues
1	Phe A:20	-	Pro A:21
2	Phe B:20	-	Pro B:21

Asymmetric Unit (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025344	R	99	Q	MASP2_HUMAN	Polymorphism	61735600	A/B	R	84	Q
2	UniProt	VAR_025345	R	118	C	MASP2_HUMAN	Polymorphism	147270785	A/B	R	103	C
3	UniProt	VAR_025346	D	120	G	MASP2_HUMAN	Disease (MASPD)	72550870	A/B	D	105	G
4	UniProt	VAR_025347	P	126	L	MASP2_HUMAN	Disease (MASPD)	56392418	A/B	P	111	L
5	UniProt	VAR_075087	T	128	M	MASP2_HUMAN	Polymorphism	141145402	A/B	T	113	M
6	UniProt	VAR_028784	H	155	R	MASP2_HUMAN	Polymorphism	2273343	A/B	H	140	R

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

Biological Unit 1 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025344	R	99	Q	MASP2_HUMAN	Polymorphism	61735600	A/B	R	84	Q
2	UniProt	VAR_025345	R	118	C	MASP2_HUMAN	Polymorphism	147270785	A/B	R	103	C
3	UniProt	VAR_025346	D	120	G	MASP2_HUMAN	Disease (MASPD)	72550870	A/B	D	105	G
4	UniProt	VAR_025347	P	126	L	MASP2_HUMAN	Disease (MASPD)	56392418	A/B	P	111	L
5	UniProt	VAR_075087	T	128	M	MASP2_HUMAN	Polymorphism	141145402	A/B	T	113	M
6	UniProt	VAR_028784	H	155	R	MASP2_HUMAN	Polymorphism	2273343	A/B	H	140	R

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

Biological Unit 2 (6, 24)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025344	R	99	Q	MASP2_HUMAN	Polymorphism	61735600	A/B	R	84	Q
2	UniProt	VAR_025345	R	118	C	MASP2_HUMAN	Polymorphism	147270785	A/B	R	103	C
3	UniProt	VAR_025346	D	120	G	MASP2_HUMAN	Disease (MASPD)	72550870	A/B	D	105	G
4	UniProt	VAR_025347	P	126	L	MASP2_HUMAN	Disease (MASPD)	56392418	A/B	P	111	L
5	UniProt	VAR_075087	T	128	M	MASP2_HUMAN	Polymorphism	141145402	A/B	T	113	M
6	UniProt	VAR_028784	H	155	R	MASP2_HUMAN	Polymorphism	2273343	A/B	H	140	R

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_CA	PS01187	Calcium-binding EGF-like domain signature.	MASP2_HUMAN	138-165	2	A:123-150 B:123-150
2	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	MASP2_HUMAN	156-167	2	A:141-152 B:141-152
3	EGF_2	PS01186	EGF-like domain signature 2.	MASP2_HUMAN	165-180	2	A:150-165 B:150-165

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_CA	PS01187	Calcium-binding EGF-like domain signature.	MASP2_HUMAN	138-165	2	A:123-150 B:123-150
2	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	MASP2_HUMAN	156-167	2	A:141-152 B:141-152
3	EGF_2	PS01186	EGF-like domain signature 2.	MASP2_HUMAN	165-180	2	A:150-165 B:150-165

Biological Unit 2 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_CA	PS01187	Calcium-binding EGF-like domain signature.	MASP2_HUMAN	138-165	4	A:123-150 B:123-150
2	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	MASP2_HUMAN	156-167	4	A:141-152 B:141-152
3	EGF_2	PS01186	EGF-like domain signature 2.	MASP2_HUMAN	165-180	4	A:150-165 B:150-165

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000400897	1d	ENSE00001833377	chr1:11107280-11107260	21	MASP2_HUMAN	1-2	2	0	-	-
1.2	ENST00000400897	2	ENSE00000818831	chr1:11107176-11106948	229	MASP2_HUMAN	2-78	77	2	A:2-63 B:3-63	62 61
1.3a	ENST00000400897	3a	ENSE00000472116	chr1:11106790-11106613	178	MASP2_HUMAN	79-138	60	2	A:64-123 B:64-123	60 60
1.3c	ENST00000400897	3c	ENSE00000743093	chr1:11105596-11105465	132	MASP2_HUMAN	138-182	45	2	A:123-167 B:123-167	45 45
1.4	ENST00000400897	4	ENSE00000472118	chr1:11103592-11103396	197	MASP2_HUMAN	182-247	66	2	A:167-168 B:167-168	2 2
1.5b	ENST00000400897	5b	ENSE00000743090	chr1:11103079-11102932	148	MASP2_HUMAN	248-297	50	0	-	-
1.6	ENST00000400897	6	ENSE00000472120	chr1:11097868-11097750	119	MASP2_HUMAN	297-336	40	0	-	-
1.7	ENST00000400897	7	ENSE00000743085	chr1:11094963-11094885	79	MASP2_HUMAN	337-363	27	0	-	-
1.8	ENST00000400897	8	ENSE00000743084	chr1:11090939-11090805	135	MASP2_HUMAN	363-408	46	0	-	-
1.9	ENST00000400897	9	ENSE00000472123	chr1:11090307-11090233	75	MASP2_HUMAN	408-433	26	0	-	-
1.10	ENST00000400897	10	ENSE00000818830	chr1:11087705-11086580	1126	MASP2_HUMAN	433-686	254	0	-	-

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:167
 aligned with MASP2_HUMAN | O00187 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:167
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       
          MASP2_HUMAN    17 PLGPKWPEPVFGRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFDLELSHLCEYDFVKLSSGAKVLATLCGQESTDTERAPGKDTFYSLGSSLDITFRSDYSNEKPFTGFEAFYAAEDIDECQVAPGEAPTCDHHCHNHLGGFYCSCRAGYVLHRNKRTCSAL 183
               SCOP domains -d1szba1 A:3-123 Mannose-binding protein associated serine protease 2, MASP2                                              d1szba2 A:124-168                             SCOP domains
               CATH domains 1szbA01 A:2-125  [code=2.60.120.290, no name defined]                                                                       1szbA02 A:126-168 Laminin                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee............eeeeeee....eeeeeeeeeee..........eeeee....eeeee................ee....eeeeeee..........eeeeeeeeee................eeeee..eeeee....eee......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------Q------------------C-G-----L-M--------------------------R---------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------EGF_CA  PDB: A:123-150      ------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL---------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------EGF_2           --- PROSITE (3)
           Transcript 1 (1) Exon 1.2  PDB: A:2-63 UniProt: 2-78 [INCOMPLETE]              Exon 1.3a  PDB: A:64-123 UniProt: 79-138                    -------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------Exon 1.3c  PDB: A:123-167 UniProt: 138-182   - Transcript 1 (2)
                 1szb A   2 PLGPKWPEPVFGRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFDLELSHLCEYDFVKLSSGAKVLATLCGQESTDTERAPGKDTFYSLGSSLDITFRSDYSNEKPFTGFEAFYAAEDIDECQVAPGEAPTCDHHCHNHLGGFYCSCRAGYVLHRNKRTCSEQ 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with MASP2_HUMAN | O00187 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:166
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      
          MASP2_HUMAN    18 LGPKWPEPVFGRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFDLELSHLCEYDFVKLSSGAKVLATLCGQESTDTERAPGKDTFYSLGSSLDITFRSDYSNEKPFTGFEAFYAAEDIDECQVAPGEAPTCDHHCHNHLGGFYCSCRAGYVLHRNKRTCSAL 183
               SCOP domains d1szbb1 B:3-123 Mannose-binding protein associated serine protease 2, MASP2                                              d1szbb2 B:124-168                             SCOP domains
               CATH domains 1szbB01 B:3-125  [code=2.60.120.290, no name defined]                                                                      1szbB02 B:126-168 Laminin                   CATH domains
           Pfam domains (1) ------CUB-1szbB01 B:9-119                                                                                            ---EGF_CA-1szbB03 B:123-165                   --- Pfam domains (1)
           Pfam domains (2) ------CUB-1szbB02 B:9-119                                                                                            ---EGF_CA-1szbB04 B:123-165                   --- Pfam domains (2)
         Sec.struct. author .........eeeee............eeeeeee.....eeeeeeeeee..........eeeeee..eeeeee................ee....eeeeeee..........eeeeeeeee.................eeeee..eeeee....eee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------Q------------------C-G-----L-M--------------------------R---------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------EGF_CA  PDB: B:123-150      ------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL---------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------EGF_2           --- PROSITE (3)
           Transcript 1 (1) Exon 1.2  PDB: B:3-63 UniProt: 2-78 [INCOMPLETE]             Exon 1.3a  PDB: B:64-123 UniProt: 79-138                    -------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------Exon 1.3c  PDB: B:123-167 UniProt: 138-182   - Transcript 1 (2)
                 1szb B   3 LGPKWPEPVFGRLASPGFPGEYANDQERRWTLTAPPGYRLRLYFTHFDLELSHLCEYDFVKLSSGAKVLATLCGQESTDTERAPGKDTFYSLGSSLDITFRSDYSNEKPFTGFEAFYAAEDIDECQVAPGEAPTCDHHCHNHLGGFYCSCRAGYVLHRNKRTCSEQ 168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Human (Homo sapiens) (195)

1a	1szbA02	A:126-168
1b	1szbB02	B:126-168

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

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

Human (Homo sapiens) (7)

2a	1szbB01	B:3-125
2b	1szbA01	A:2-125

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CUB (11)

Family: CUB (11)

Homo sapiens (Human) (8)

1a	CUB-1szbB01	B:9-119
1b	CUB-1szbB02	B:9-119

Clan: EGF (60)

Family: EGF_CA (18)

Homo sapiens (Human) (14)

2a	EGF_CA-1szbB03	B:123-165
2b	EGF_CA-1szbB04	B:123-165

Asymmetric Unit(hide GO term definitions)

Chain A,B (MASP2_HUMAN | O00187)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0001855	complement component C4b binding	Interacting selectively and non-covalently with the C4b product of the classical complement cascade.
	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:0001867	complement activation, lectin pathway	Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes 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: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: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.

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	1szb
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	MASP2_HUMAN \| O00187	:	1q3x 1zjk 3tvj 4fxg 5jpm

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