4A2Y - JenaLib

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Title :   STRUCTURE OF THE HUMAN EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WITH CITRATE ANIONS

Authors :   E. Boix, D. Pulido, M. Moussaoui, V. Nogues, S. Russi

Date :   29 Sep 11 (Deposition) - 27 Jun 12 (Release) - 27 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Hydrolase, Oxidoreductase, Antimicrobial, Cytotoxic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Boix, D. Pulido, M. Moussaoui, V. Nogues, S. Russi
The Sulfate-Binding Site Structure Of The Human Eosinophil Cationic Protein As Revealed By A New Crystal Form.
J. Struct. Biol. V. 179 1 2012
PubMed-ID: 22579681 | Reference-DOI: 10.1016/J.JSB.2012.04.023

Molecule 1 - EOSINOPHIL CATIONIC PROTEIN
	Cell	:	EOSINOPHIL
	Chains	:	A, B
	EC Number	:	3.1.27.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11C/ECP
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET11C
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ECP, RIBONUCLEASE 3, RNASE 3

		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 (2, 6)

No.	Name	Count	Type	Full Name
1	CIT	5	Ligand/Ion	CITRIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CIT	3	Ligand/Ion	CITRIC ACID
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:46 , ASN A:50 , SER A:74 , ARG A:75 , PHE A:76 , VAL A:78 , TYR A:107 , HOH A:2119 , HOH A:2121 , HOH A:2126 , HOH A:2129 , HOH A:2222 , HOH A:2223 , ARG B:121	BINDING SITE FOR RESIDUE CIT A 301
2	AC2	SOFTWARE	ARG A:34 , LYS A:38 , ASN A:39 , HOH A:2092 , HOH A:2224	BINDING SITE FOR RESIDUE CIT A 302
3	AC3	SOFTWARE	ARG A:61 , ARG A:66 , HOH A:2149 , THR B:46 , ASN B:50 , VAL B:54 , ASN B:57 , SER B:74 , ARG B:75 , PHE B:76 , VAL B:78 , TYR B:107 , HOH B:2047 , HOH B:2048	BINDING SITE FOR RESIDUE CIT B 301
4	AC4	SOFTWARE	ARG B:34 , CYS B:37 , LYS B:38 , ASN B:39 , HOH B:2078 , HOH B:2079	BINDING SITE FOR RESIDUE CIT B 302
5	AC5	SOFTWARE	ARG A:45 , HOH A:2057 , HOH A:2058 , HOH A:2059 , ARG B:114 , PRO B:116 , HOH B:2064 , HOH B:2065 , HOH B:2066 , HOH B:2082	BINDING SITE FOR RESIDUE CIT B 303
6	AC6	SOFTWARE	ARG A:97 , HOH A:2065 , HOH A:2066 , HOH A:2188 , HOH A:2189 , HOH A:2226 , HOH A:2227 , HOH A:2228 , ARG B:77 , HOH B:2050 , HOH B:2051	BINDING SITE FOR RESIDUE MPD A1134

Asymmetric Unit

No.	Residues
1	A:23	-	A:83
2	A:37	-	A:96
3	A:55	-	A:111
4	A:62	-	A:71
5	B:23	-	B:83
6	B:37	-	B:96
7	B:55	-	B:111
8	B:62	-	B:71

(no "Cis Peptide Bond" information available for 4A2Y)

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)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	ECP_HUMAN	64-70	2	A:37-43 B:37-43

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	ECP_HUMAN	64-70	1	A:37-43 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	ECP_HUMAN	64-70	1	- B:37-43

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000304639	1	ENSE00001137146	chr14:21359558-21359610	53	ECP_HUMAN	-	0	0	-	-
1.2	ENST00000304639	2	ENSE00001124180	chr14:21359841-21360507	667	ECP_HUMAN	1-162	162	2	A:1-133 B:1-133	133 133

Asymmetric Unit

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	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: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 d4a2ya_ A: Eosinophil cationic protein (ECP), ribonuclease 3                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....hhhhhhhhhhh.......eeeee..hhhhhhhhh...............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
                 4a2y 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 d4a2yb_ B: Eosinophil cationic protein (ECP), ribonuclease 3                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- 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: B:1-133 UniProt: 1-162 [INCOMPLETE]                                                                                    Transcript 1
                 4a2y B   1 RPPQFTRAQWFAIQHISLNPPRCTIAMRAINNYRWRCKNQNTFLRTTFANVVNVCGNQSIRCPHNRTLNNCHRSRFRVPLLHCDLINPGAQNISNCRYADRPGRRFYVVACDNRDPRDSPRYPVVPVHLDTTI 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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	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: RNase A-like (356)

Superfamily: RNase A-like (356)

Family: Ribonuclease A-like (347)

Protein domain: Eosinophil cationic protein (ECP), ribonuclease 3 (7)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d4a2ya_	A:
1b	d4a2yb_	B:

(no "CATH Domain" information available for 4A2Y)

(no "Pfam Domain" information available for 4A2Y)

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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	4a2y
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	3.1.27.-
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UniProtKB/Swiss-Prot
	ECP_HUMAN \| P12724	:	1dyt 1h1h 1qmt 2kb5 2lvz 4a2o 4owz 4oxb 4oxf 4x08

1dyt	X-RAY CRYSTAL STRUCTURE OF ECP (RNASE 3) AT 1.75 A
1h1h	CRYSTAL STRUCTURE OF EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WITH 2',5'-ADP AT 2.0 A RESOLUTION REVEALS THE DETAILS OF THE RIBONUCLEOLYTIC ACTIVE SITE
1qmt	RECOMBINANT HUMAN EOSINOPHIL CATIONIC PROTEIN
4a2o	STRUCTURE OF THE HUMAN EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WITH SULFATE ANIONS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

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Exons (1, 2)

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Gene Ontology (15, 15)

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