1DYT - JenaLib

Title :   X-RAY CRYSTAL STRUCTURE OF ECP (RNASE 3) AT 1.75 A

Authors :   G. Mallorqui-Fernandez, J. Pous, R. Peracaula, T. Maeda, H. Tada, H. Yamada, M. Seno, R. De Llorens, F. X. Gomis-Rueth, M. Coll

Date :   08 Feb 00 (Deposition) - 08 Feb 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Hydrolase, Eosinophil Cationic Protein, Ecp, Rnase 3 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Mallorqui-Fernandez, J. Pous, R. Peracaula, T. Maeda, H. Tada, H. Yamada, M. Seno, R. De Llorens, F. X. Gomis-Rueth, M. Coll
Three-Dimensional Crystal Structure Of Human Eosinophil Cationic Protein (Rnase 3) At 1. 75 A Resolution.
J. Mol. Biol. V. 300 1297 2000
PubMed-ID: 10903870 | Reference-DOI: 10.1006/JMBI.2000.3939

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:34 , CIT B:302 , HOH B:2144	BINDING SITE FOR RESIDUE FE B 300
2	AC2	SOFTWARE	CIT A:302	BINDING SITE FOR RESIDUE FE A 300
3	AC3	SOFTWARE	THR A:46 , ASN A:50 , VAL A:54 , SER A:74 , ARG A:75 , PHE A:76 , VAL A:78 , TYR A:107 , HOH A:2109 , HOH A:2180 , HOH A:2181 , HOH A:2182 , ARG B:121	BINDING SITE FOR RESIDUE CIT A 301
4	AC4	SOFTWARE	ARG A:61 , ARG A:66 , THR B:46 , ASN B:50 , VAL B:54 , SER B:74 , ARG B:75 , PHE B:76 , VAL B:78 , TYR B:107 , HOH B:2083 , HOH B:2142 , HOH B:2143	BINDING SITE FOR RESIDUE CIT B 301
5	AC5	SOFTWARE	ARG A:34 , LYS A:38 , ASN A:39 , GLN A:40 , FE A:300 , HOH A:2094 , HOH A:2096 , HOH A:2183 , HOH A:2184 , HOH A:2185	BINDING SITE FOR RESIDUE CIT A 302
6	AC6	SOFTWARE	ARG B:34 , ARG B:36 , CYS B:37 , LYS B:38 , ASN B:39 , GLN B:40 , FE B:300 , HOH B:2068 , HOH B:2144 , HOH B:2145 , HOH B:2146 , HOH B:2147	BINDING SITE FOR RESIDUE CIT B 302

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014109	R	72	C	ECP_HUMAN	Polymorphism	151169198	A/B	R	45	C
2	UniProt	VAR_013149	T	124	R	ECP_HUMAN	Polymorphism	2073342	A/B	R	97	R
3	UniProt	VAR_029017	G	130	R	ECP_HUMAN	Polymorphism	12147890	A/B	G	103	R

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_014109	R	72	C	ECP_HUMAN	Polymorphism	151169198	A	R	45	C
2	UniProt	VAR_013149	T	124	R	ECP_HUMAN	Polymorphism	2073342	A	R	97	R
3	UniProt	VAR_029017	G	130	R	ECP_HUMAN	Polymorphism	12147890	A	G	103	R

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_014109	R	72	C	ECP_HUMAN	Polymorphism	151169198	B	R	45	C
2	UniProt	VAR_013149	T	124	R	ECP_HUMAN	Polymorphism	2073342	B	R	97	R
3	UniProt	VAR_029017	G	130	R	ECP_HUMAN	Polymorphism	12147890	B	G	103	R

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

PROSITE Motifs (1, 2)

Exons (1, 2)

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:133
 aligned with ECP_HUMAN | P12724 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:133
                                    37        47        57        67        77        87        97       107       117       127       137       147       157   
            ECP_HUMAN    28 RPPQFTRAQWFAIQHISLNPPRCTIAMRAINNYRWRCKNQNTFLRTTFANVVNVCGNQSIRCPHNRTLNNCHRSRFRVPLLHCDLINPGAQNISNCTYADRPGRRFYVVACDNRDPRDSPRYPVVPVHLDTTI 160
               SCOP domains d1dyta_ A: Eosinophil cationic protein (ECP), ribonuclease 3                                                                          SCOP domains
               CATH domains 1dytA00 A:1-133 P-30 Protein                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....hhhhhhhhhhh.......eeeee..hhhhhhhhh...ee..........eee....eeeeeeee............eeeeeeee.eeeeeee..........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------C---------------------------------------------------R-----R------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------RNASE_P------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-133 UniProt: 1-162 [INCOMPLETE]                                                                                    Transcript 1
                 1dyt A   1 RPPQFTRAQWFAIQHISLNPPRCTIAMRAINNYRWRCKNQNTFLRTTFANVVNVCGNQSIRCPHNRTLNNCHRSRFRVPLLHCDLINPGAQNISNCRYADRPGRRFYVVACDNRDPRDSPRYPVVPVHLDTTI 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with ECP_HUMAN | P12724 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:133
                                    37        47        57        67        77        87        97       107       117       127       137       147       157   
            ECP_HUMAN    28 RPPQFTRAQWFAIQHISLNPPRCTIAMRAINNYRWRCKNQNTFLRTTFANVVNVCGNQSIRCPHNRTLNNCHRSRFRVPLLHCDLINPGAQNISNCTYADRPGRRFYVVACDNRDPRDSPRYPVVPVHLDTTI 160
               SCOP domains d1dytb_ B: Eosinophil cationic protein (ECP), ribonuclease 3                                                                          SCOP domains
               CATH domains 1dytB00 B:1-133 P-30 Protein                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....hhhhhhhhhhh.......eeeee..hhhhhhhhh...ee..........eee....eeeeeeee......hhhhh.eeeeeeee.eeeeeee..........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------C---------------------------------------------------R-----R------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------RNASE_P------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-133 UniProt: 1-162 [INCOMPLETE]                                                                                    Transcript 1
                 1dyt B   1 RPPQFTRAQWFAIQHISLNPPRCTIAMRAINNYRWRCKNQNTFLRTTFANVVNVCGNQSIRCPHNRTLNNCHRSRFRVPLLHCDLINPGAQNISNCRYADRPGRRFYVVACDNRDPRDSPRYPVVPVHLDTTI 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ECP_HUMAN | P12724)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	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:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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