2BRS - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   EMBP HEPARIN COMPLEX

Authors :   G. J. Swaminathan, D. G. Myszka, P. S. Katsamba, L. E. Ohnuki, G. J. Gleich, K. R. Acharya

Date :   11 May 05 (Deposition) - 26 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Antibiotic, Embp, Eosinophil, Eosinophil Granule Protein, Glycoprotein, Heparin-Binding, Immune Response, Lectin, Proteoglycan, Signal, Heparin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. J. Swaminathan, D. G. Myszka, P. S. Katsamba, L. E. Ohnuki, G. J. Gleich, K. R. Acharya
Eosinophil-Granule Major Basic Protein, A C-Type Lectin, Binds Heparin
Biochemistry V. 44 14152 2005
PubMed-ID: 16245931 | Reference-DOI: 10.1021/BI051112B

Molecule 1 - EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
	Cell	:	EOSINOPHIL
	Chains	:	A, B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	HEPARIN SULPHATE
	Synonym	:	MBP, EMBP, PREGNANCY ASSOCIATED MAJOR BASIC PROTEIN, PROTEOGLYCAN 2 BONE MARROW, BMPG

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	IDU	1	Ligand/Ion	1,4-DIDEOXY-O2-SULFO-GLUCURONIC ACID
2	SGN	1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	IDU	1	Ligand/Ion	1,4-DIDEOXY-O2-SULFO-GLUCURONIC ACID
2	SGN	1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	IDU	-1	Ligand/Ion	1,4-DIDEOXY-O2-SULFO-GLUCURONIC ACID
2	SGN	-1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:83 , HOH A:2050 , HOH A:2051 , HOH A:2052 , HOH A:2053 , HOH A:2054 , SGN A:5702 , CYS B:96 , ARG B:98 , TYR B:101 , ARG B:103 , ARG B:109	BINDING SITE FOR RESIDUE IDU A1623
02	AC2	SOFTWARE	ALA A:82 , HIS A:83 , IDU A:1623 , HOH A:2055 , ALA B:81 , ALA B:82 , HIS B:83 , PRO B:85 , ARG B:88 , HIS B:106	BINDING SITE FOR RESIDUE SGN A5702
03	AC3	SOFTWARE	GLY A:90 , HIS A:91 , HIS A:106 , CYS A:107 , HOH A:2045 , HOH A:2046	BINDING SITE FOR RESIDUE SO4 A1118
04	AC4	SOFTWARE	ARG A:3 , ARG A:65 , ARG A:88 , HIS A:91 , ARG A:104 , HOH A:2039 , HOH A:2047 , HOH A:2048	BINDING SITE FOR RESIDUE SO4 A1119
05	AC5	SOFTWARE	ARG A:103 , ARG A:104 , ALA A:105 , HIS A:106 , ARG A:109 , HOH A:2049	BINDING SITE FOR RESIDUE SO4 A1120
06	AC6	SOFTWARE	GLN A:84 , PRO A:85 , TRP A:86 , SER A:87 , ARG A:88	BINDING SITE FOR RESIDUE SO4 A1121
07	AC7	SOFTWARE	LEU A:10 , THR A:12 , GLN A:15 , ARG A:110	BINDING SITE FOR RESIDUE SO4 A1122
08	AC8	SOFTWARE	GLY B:90 , HIS B:91 , ALA B:105 , HIS B:106 , CYS B:107 , HOH B:2033 , HOH B:2035	BINDING SITE FOR RESIDUE SO4 B1118
09	AC9	SOFTWARE	ARG B:3 , HIS B:91 , ARG B:104 , TYR B:117 , HOH B:2037	BINDING SITE FOR RESIDUE SO4 B1119
10	BC1	SOFTWARE	HIS B:83 , PRO B:85 , TRP B:86 , SER B:87	BINDING SITE FOR RESIDUE SO4 B1120

Asymmetric Unit

No.	Residues
1	A:20	-	A:115
2	A:92	-	A:107
3	B:20	-	B:115
4	B:92	-	B:107

(no "Cis Peptide Bond" information available for 2BRS)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036401	R	179	C	PRG2_HUMAN	Unclassified	142359007	A/B	R	74	C
2	CancerSNP	VAR_PRG2_HUMAN_CCDS7955_1_01 *	R	179	C	PRG2_HUMAN	Disease (Colorectal cancer)	---	A/B	R	74	C
3	UniProt	VAR_060729	H	206	Y	PRG2_HUMAN	Polymorphism	536455	A/B	Y	101	Y
	* ID not provided by source

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036401	R	179	C	PRG2_HUMAN	Unclassified	142359007	A	R	74	C
2	CancerSNP	VAR_PRG2_HUMAN_CCDS7955_1_01 *	R	179	C	PRG2_HUMAN	Disease (Colorectal cancer)	---	A	R	74	C
3	UniProt	VAR_060729	H	206	Y	PRG2_HUMAN	Polymorphism	536455	A	Y	101	Y
	* ID not provided by source

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036401	R	179	C	PRG2_HUMAN	Unclassified	142359007	B	R	74	C
2	CancerSNP	VAR_PRG2_HUMAN_CCDS7955_1_01 *	R	179	C	PRG2_HUMAN	Disease (Colorectal cancer)	---	B	R	74	C
3	UniProt	VAR_060729	H	206	Y	PRG2_HUMAN	Polymorphism	536455	B	Y	101	Y
	* ID not provided by source

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	PRG2_HUMAN	109-221	2	A:4-116 B:4-116
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	PRG2_HUMAN	197-220	2	A:92-115 B:92-115

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	PRG2_HUMAN	109-221	1	A:4-116 -
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	PRG2_HUMAN	197-220	1	A:92-115 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	PRG2_HUMAN	109-221	1	- B:4-116
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	PRG2_HUMAN	197-220	1	- B:92-115

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000311862	1a	ENSE00002185412	chr11:57158130-57158069	62	PRG2_HUMAN	-	0	0	-	-
1.2	ENST00000311862	2	ENSE00002191966	chr11:57157429-57157360	70	PRG2_HUMAN	1-20	20	0	-	-
1.3b	ENST00000311862	3b	ENSE00002165885	chr11:57156790-57156483	308	PRG2_HUMAN	20-122	103	2	A:3-17 B:3-17	15 15
1.3d	ENST00000311862	3d	ENSE00001027254	chr11:57156181-57156050	132	PRG2_HUMAN	123-166	44	2	A:18-61 B:18-61	44 44
1.4	ENST00000311862	4	ENSE00001174512	chr11:57155338-57155227	112	PRG2_HUMAN	167-204	38	2	A:62-99 B:62-99	38 38
1.5d	ENST00000311862	5d	ENSE00001309153	chr11:57155006-57154267	740	PRG2_HUMAN	204-222	19	2	A:99-117 B:99-117	19 19

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
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Chain A from PDB  Type:PROTEIN  Length:115
 aligned with PRG2_HUMAN | P13727 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:115
                                   117       127       137       147       157       167       177       187       197       207       217     
           PRG2_HUMAN   108 RYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWAAHQPWSRGGHCVALCTRGGHWRRAHCLRRLPFICSY 222
               SCOP domains d2brsa_ A: Eosinophil major basic protein                                                                           SCOP domains
               CATH domains 2brsA00 A:3-117 Mannose-Binding Protein A, subunit A                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhh.ee....hhhhhhhhhhhhh.....eeeeeeeee......eeee......................eeeee.....eeee.....eeeeee. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------C--------------------------Y---------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------C------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) -C_TYPE_LECTIN_2  PDB: A:4-116 UniProt: 109-221                                                                   - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------C_TYPE_LECTIN_1         -- PROSITE (2)
           Transcript 1 (1) Exon 1.3b      Exon 1.3d  PDB: A:18-61 UniProt: 123-166    Exon 1.4  PDB: A:62-99                ------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------Exon 1.5d           Transcript 1 (2)
                 2brs A   3 RYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWAAHQPWSRGGHCVALCTRGGYWRRAHCLRRLPFICSY 117
                                    12        22        32        42        52        62        72        82        92       102       112

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with PRG2_HUMAN | P13727 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:115
                                   117       127       137       147       157       167       177       187       197       207       217     
           PRG2_HUMAN   108 RYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWAAHQPWSRGGHCVALCTRGGHWRRAHCLRRLPFICSY 222
               SCOP domains d2brsb_ B: Eosinophil major basic protein                                                                           SCOP domains
               CATH domains 2brsB00 B:3-117 Mannose-Binding Protein A, subunit A                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhh.ee....hhhhhhhhhhhh......eeeeeeeeee....eeeee......................eeeee.....eeee.....eeeeee. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------C--------------------------Y---------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------C------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) -C_TYPE_LECTIN_2  PDB: B:4-116 UniProt: 109-221                                                                   - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------C_TYPE_LECTIN_1         -- PROSITE (2)
           Transcript 1 (1) Exon 1.3b      Exon 1.3d  PDB: B:18-61 UniProt: 123-166    Exon 1.4  PDB: B:62-99                ------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------Exon 1.5d           Transcript 1 (2)
                 2brs B   3 RYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWAAHQPWSRGGHCVALCTRGGYWRRAHCLRRLPFICSY 117
                                    12        22        32        42        52        62        72        82        92       102       112

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	-	→ 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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: C-type lectin domain (182)

Protein domain: Eosinophil major basic protein (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2brsa_	A:
1b	d2brsb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Mannose-Binding Protein A; Chain A (180)

Homologous Superfamily: Mannose-Binding Protein A, subunit A (180)

Human (Homo sapiens) (80)

1a	2brsA00	A:3-117
1b	2brsB00	B:3-117

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRG2_HUMAN | P13727)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
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:0002215	defense response to nematode	A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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:0032693	negative regulation of interleukin-10 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production.
	GO:0032753	positive regulation of interleukin-4 production	Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
	GO:0042035	regulation of cytokine biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines.
cellular component
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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.
	GO:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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	PRG2_HUMAN \| P13727	:	1h8u 4qxx

1h8u	CRYSTAL STRUCTURE OF THE EOSINOPHIL MAJOR BASIC PROTEIN AT 1.8E: AN ATYPICAL LECTIN WITH A PARADIGM SHIFT IN SPECIFICITY

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (3, 10)

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SS Bonds (4, 4)

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