1DZA - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   3-D STRUCTURE OF A HP-RNASE

Authors :   J. Pous, A. Canals, S. S. Terzyan, A. Guasch, A. Benito, M. Ribo, M. Vilanova, M. Coll

Date :   21 Feb 00 (Deposition) - 16 Feb 01 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Hydrolase, Ribonuclease, Rnase, Human Pancreatic Ribonuclease, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Pous, A. Canals, S. S. Terzyan, A. Guasch, A. Benito, M. Ribo, M. Vilanova, M. Coll
Three-Dimensional Structure Of A Human Pancreatic Ribonuclease Variant, A Step Forward In The Design Of Cytotoxic Ribonucleases
J. Mol. Biol. V. 303 49 2000
PubMed-ID: 11021969 | Reference-DOI: 10.1006/JMBI.2000.4506

Molecule 1 - RIBONUCLEASE 1
	Chains	:	A, B
	EC Number	:	3.1.27.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	PM7
	Expression System Plasmid	:	PM7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PM7
	Mutation	:	YES
	Organ	:	PANCREAS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	100A FORMILMETHIONINE (FME)
	Other Details - Source	:	SYNTHETIC GENE
	Synonym	:	RNASE 1, HP-RNASE

		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 (1, 1)

No.	Name	Count	Type	Full Name
1	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FME	-1	Mod. Amino Acid	N-FORMYLMETHIONINE

(no "Site" information available for 1DZA)

Asymmetric Unit

No.	Residues
1	A:126	-	A:184
2	A:140	-	A:195
3	A:158	-	A:210
4	A:165	-	A:172
5	B:126	-	B:184
6	B:140	-	B:195
7	B:158	-	B:210
8	B:165	-	B:172

Asymmetric Unit

No.	Residues
1	Tyr A:192	-	Pro A:193
2	Ser A:213	-	Pro A:214
3	Tyr B:192	-	Pro B:193
4	Ser B:213	-	Pro B:214

(no "SAP(SNP)/Variant" information available for 1DZA)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	2	A:140-146 B:140-146

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	1	A:140-146 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	1	- B:140-146

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000397970	1c	ENSE00001915577	chr14:21271007-21270956	52	RNAS1_HUMAN	-	0	0	-	-
1.2c	ENST00000397970	2c	ENSE00001530999	chr14:21270478-21270408	71	RNAS1_HUMAN	-	0	0	-	-
1.3a	ENST00000397970	3a	ENSE00001837426	chr14:21270252-21269542	711	RNAS1_HUMAN	1-165	165	2	A:100-225 (gaps) B:102-226 (gaps)	126 125

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:121
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:126
                                    37        47        57        67        77        87        97       107       117       127       137       147      
          RNAS1_HUMAN    28 GKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVE 153
               SCOP domains d1dzaa_ A: Ribonuc     lease A (also ribonuclease B, S)                                                                        SCOP domains
               CATH domains -1dzaA00 A:101-225      P-30 Protein                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....-----.hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeee.........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------RNASE_P------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3a  PDB: A:100-225 (gaps) UniProt: 1-165 [INCOMPLETE]                                                                   Transcript 1
                 1dza A 100 mKESAAAKFERQHMDSGN-----STYCNQMMRRRNMTQGRCKPVNTFVHESLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVE 225
                            |      109       | -   |   129       139       149       159       169       179       189       199       209       219      
                            |              117   123                                                                                                      
                          100-FME

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:125
                                    39        49        59        69        79        89        99       109       119       129       139       149     
          RNAS1_HUMAN    30 ESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 154
               SCOP domains d1dzab_ B: Ribon    uclease A (also ribonuclease B, S)                                                                        SCOP domains
               CATH domains 1dzaB00 B:102-22    6 P-30 Protein                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....----..hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeee.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------RNASE_P-------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3a  PDB: B:102-226 (gaps) UniProt: 1-165 [INCOMPLETE]                                                                  Transcript 1
                 1dza B 102 ESAAAKFERQHMDSGN----SSTYCNQMMRRRNMTQGRCKPVNTFVHESLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 226
                                   111     |   -|      131       141       151       161       171       181       191       201       211       221     
                                         117  122

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: Ribonuclease A (also ribonuclease B, S) (173)

Human (Homo sapiens), des1-7 [TaxId: 9606] (8)

1a	d1dzaa_	A:
1b	d1dzab_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: P-30 Protein (299)

Homologous Superfamily: P-30 Protein (299)

Human (Homo sapiens) (46)

1a	1dzaB00	B:102-226
1b	1dzaA00	A:101-225

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (RNAS1_HUMAN | P07998)

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: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:0004522	ribonuclease A activity	Catalysis of the endonucleolytic cleavage of RNA to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	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.

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	Ligands, Modified Residues, Ions
		FME	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1dza)

	Cis Peptide Bonds
		Ser A:213 - Pro A:214	[ RasMol ]
		Ser B:213 - Pro B:214	[ RasMol ]
		Tyr A:192 - Pro A:193	[ RasMol ]
		Tyr B:192 - Pro B:193	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1dza
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	3.1.27.5
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	RNAS1_HUMAN \| P07998	:	1e21 1h8x 1z7x 2e0j 2e0l 2e0m 2e0o 2k11 2q4g 3f8g 4kxh

(no "Related Entries Specified in the PDB File" available for 1DZA)

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

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