1H8X - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   DOMAIN-SWAPPED DIMER OF A HUMAN PANCREATIC RIBONUCLEASE VARIANT

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

Date :   16 Feb 01 (Deposition) - 14 Feb 02 (Release) - 21 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

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

Reference :   A. Canals, J. Pous, A. Guasch, A. Benito, M. Ribo, M. Vilanova, M. Coll
The Structure Of An Engineered Domain-Swapped Ribonuclease Dimer And Its Implications For The Evolution Of Proteins Toward Oligomerization
Structure V. 9 967 2001
PubMed-ID: 11591351 | Reference-DOI: 10.1016/S0969-2126(01)00659-1

Molecule 1 - RIBONUCLEASE 1
	Chains	:	A, B
	EC Number	:	3.1.27.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	PM8
	Expression System Plasmid	:	PM8
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNASE 1, HP-RNASE
	Gene	:	PM8
	Mutation	:	YES
	Organ	:	PANCREAS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	RESIDIE 100 IS A FORMILMETHIONINE (FME)
	Other Details - Source	:	SYNTHETIC GENE
	Plasmid	:	PM8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1H8X)

(no "Site" information available for 1H8X)

Asymmetric/Biological 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/Biological 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 1H8X)

Asymmetric/Biological 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

Asymmetric/Biological 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:101-226 B:101-226	126 126

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:126
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:126
                                    38        48        58        68        78        88        98       108       118       128       138       148      
          RNAS1_HUMAN    29 KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 154
               SCOP domains d1h8xa_ A: Ribonuclease A (also ribonuclease B, S)                                                                             SCOP domains
               CATH domains 1h8xA00 A:101-226 P-30 Protein                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee.......eeee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P-------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3a  PDB: A:101-226 UniProt: 1-165 [INCOMPLETE]                                                                          Transcript 1
                 1h8x A 101 KESAAAKFERQHMDSGNSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSQKERHIIVACEGSPYVPVHFDASVED 226
                                   110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:126
                                    38        48        58        68        78        88        98       108       118       128       138       148      
          RNAS1_HUMAN    29 KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 154
               SCOP domains d1h8xb_ B: Ribonuclease A (also ribonuclease B, S)                                                                             SCOP domains
               CATH domains 1h8xB00 B:101-226 P-30 Protein                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeee.eeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P-------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3a  PDB: B:101-226 UniProt: 1-165 [INCOMPLETE]                                                                          Transcript 1
                 1h8x B 101 KESAAAKFERQHMDSGNSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSQKERHIIVACEGSPYVPVHFDASVED 226
                                   110       120       130       140       150       160       170       180       190       200       210       220

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(

)

Folds(

)

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	d1h8xa_	A:
1b	d1h8xb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: P-30 Protein (299)

Homologous Superfamily: P-30 Protein (299)

Human (Homo sapiens) (46)

1a	1h8xA00	A:101-226
1b	1h8xB00	B:101-226

(no "Pfam Domain" information available for 1H8X)

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1h8x)

	Sites
(no "Sites" information available for 1h8x)

	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 ]

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

1e21	RIBONUCLEASE 1 DES1-7 CRYSTAL STRUCTURE AT 1.9A

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

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Gene Ontology (10, 10)

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