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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ARH-I, AN ANGIOGENIN/RNASE A CHIMERA

Authors :   D. E. Holloway, R. Shapiro, M. C. Hares, D. D. Leonidas, K. R. Acharya

Date :   06 Feb 02 (Deposition) - 22 Aug 02 (Release) - 15 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Pancreatic Ribonuclease, Angiogenesis, Angiogenin, Chimera, Hybrid, Homolog Scanning Mutagenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. E. Holloway, R. Shapiro, M. C. Hares, D. D. Leonidas, K. R. Acharya
Guest-Host Crosstalk In An Angiogenin-Rnase A Chimeric Protein
Biochemistry V. 41 10482 2002
PubMed-ID: 12173935 | Reference-DOI: 10.1021/BI026151R

Molecule 1 - ANGIOGENIN
	Chains	:	A
	EC Number	:	3.1.27.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	W3110
	Expression System Taxid	:	316407
	Expression System Vector	:	PANG3
	Mutation	:	YES
	Organism Common	:	HUMAN, BOVINE
	Organism Scientific	:	HOMO SAPIENS, BOS TAURUS
	Organism Taxid	:	9606, 9913
	Other Details	:	SUBSTITUTED SEQUENCE IS BOVINE. SYNTHETIC GENE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:8 , GLN A:12 , HIS A:13 , LYS A:40 , HIS A:116 , LEU A:117 , GLN A:119 , HOH A:2061 , HOH A:2062	BINDING SITE FOR RESIDUE CIT A3001

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:83
2	A:39	-	A:94
3	A:57	-	A:109
4	A:64	-	A:71

Asymmetric/Biological Unit

No.	Residues
1	Ser A:37	-	Pro A:38
2	Pro A:92	-	Pro A:93

Asymmetric/Biological Unit (14, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_044147	Q	36	L	ANGI_HUMAN	Disease (ALS9)	121909535	A	Q	12	L
02	UniProt	VAR_073021	Y	38	H	ANGI_HUMAN	Disease (ALS9)	---	A	Y	14	H
03	UniProt	VAR_044148	K	41	E	ANGI_HUMAN	Disease (ALS9)	121909537	A	K	17	E
04	UniProt	VAR_044149	K	41	I	ANGI_HUMAN	Disease (ALS9)	121909536	A	K	17	I
05	UniProt	VAR_073022	D	46	G	ANGI_HUMAN	Disease (ALS9)	---	A	D	22	G
06	UniProt	VAR_044150	S	52	N	ANGI_HUMAN	Disease (ALS9)	121909542	A	S	28	N
07	UniProt	VAR_044151	R	55	K	ANGI_HUMAN	Disease (ALS9)	121909538	A	R	31	K
08	UniProt	VAR_044152	C	63	W	ANGI_HUMAN	Disease (ALS9)	121909539	A	C	39	W
09	UniProt	VAR_044153	K	64	I	ANGI_HUMAN	Disease (ALS9)	121909540	A	K	40	I
10	UniProt	VAR_044154	I	70	V	ANGI_HUMAN	Polymorphism	121909541	A	I	46	V
11	UniProt	VAR_013148	K	84	E	ANGI_HUMAN	Polymorphism	17560	A	K	60	E
12	UniProt	VAR_044155	P	136	L	ANGI_HUMAN	Disease (ALS9)	121909543	A	P	114	L
13	UniProt	VAR_044156	V	137	I	ANGI_HUMAN	Disease (ALS9)	121909544	A	V	115	I
14	UniProt	VAR_044157	H	138	R	ANGI_HUMAN	Disease (ALS9)	---	A	H	116	R

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	ANGI_HUMAN	63-69	1	A:39-45

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000397990	2a	ENSE00002201651	chr14:21156932-21157033	102	ANGI_HUMAN	-	0	0	-	-
1.3c	ENST00000397990	3c	ENSE00001758396	chr14:21161706-21162338	633	ANGI_HUMAN	1-153	153	1	A:1-123	123

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
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Chain A from PDB  Type:PROTEIN  Length:123
 aligned with ANGI_HUMAN | P03950 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:123
                                                                                       85 86                                                           
                                    34        44        54        64        74        84|  |    92       102       112       122       132       142   
           ANGI_HUMAN    25 QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKN--GNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR 145
               SCOP domains d1gv7a_ A: Angiogenin                                                                                                       SCOP domains
               CATH domains -1gv7A00 A:2-123 P-30 Protein                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhhhhhhhhh........eeeee..hhhhhhhhhhh.ee........eee....eeeeeeee..........eeeeeeee..eeeee..eeeee.hhhhh Sec.struct. author
             SAPs(SNPs) (1) -----------L-H--E----G-----N--K-------WI-----V-------------E-----------------------------------------------------LIR------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------I---------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3c  PDB: A:1-123 UniProt: 1-153 [INCOMPLETE]                                                                         Transcript 1
                 1gv7 A   1 xDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICSQKNVACKNGQTNCYISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR 123
                            |       10        20        30        40        50        60        70        80        90       100       110       120   
                            |                                                                                                                          
                            1-PCA

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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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: Angiogenin (32)

Human (Homo sapiens) [TaxId: 9606] (30)

d1gv7a_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: P-30 Protein (299)

Homologous Superfamily: P-30 Protein (299)

Human, bovine (Homo sapiens, bos taurus) (1)

1gv7A00

A:2-123

(no "Pfam Domain" information available for 1GV7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ANGI_HUMAN | P03950)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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.
	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:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0030041	actin filament polymerization	Assembly of actin filaments by the addition of actin monomers to a filament.
	GO:0032431	activation of phospholipase A2 activity	Any process that initiates the activity of the inactive enzyme phospholipase A2.
	GO:0007202	activation of phospholipase C activity	The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
	GO:0032148	activation of protein kinase B activity	Any process that initiates the activity of the inactive enzyme protein kinase B.
	GO:0034332	adherens junction organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	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:0019732	antifungal humoral response	An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
	GO:0007154	cell communication	Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	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:0006651	diacylglycerol biosynthetic process	The chemical reactions and pathways resulting in the formation of diacylglycerol, a glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group.
	GO:0042592	homeostatic process	Any biological process involved in the maintenance of an internal steady state.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0048662	negative regulation of smooth muscle cell proliferation	Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0001556	oocyte maturation	A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization.
	GO:0001541	ovarian follicle development	The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
	GO:0001890	placenta development	The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0042327	positive regulation of phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
	GO:0050714	positive regulation of protein secretion	Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0001878	response to yeast	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species.
cellular component
	GO:0032311	angiogenin-PRI complex	A stable heterodimer of angiogenin and placental ribonuclease inhibitor; interaction between angiogenin and PRI prevents angiogenin binding to its receptor to stimulate angiogenesis.
	GO:0005605	basal lamina	A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
	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: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.
	GO:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	1gv7
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1a4y	RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX
1ang	ANGIOGENIN
1awz	3D SOLUTION STRUCTURE OF HUMAN ANGIOGENIN DETERMINED BY 1H, 15N NMR SPECTROSCOPY, 30 STRUCTURES
1b1e	CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT K40Q
1b1i	CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN
1b1j	CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT H13A.
1h52	BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY
1h53	BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY
1hby	BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY
2ang	CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN OF THE MET(-1) FORM

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (1, 1)

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