3EH8 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF Y2 I-ANII VARIANT (F13Y/S111Y)/DNA COMPLEX WITH CALCIUM

Authors :   R. Takeuchi, B. L. Stoddard

Date :   11 Sep 08 (Deposition) - 13 Jan 09 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)
Biol. Unit 3: G,H,I  (1x)

Keywords :   Protein-Dna Complex, Endonuclease, Hydrolase, Intron Homing, Mitochondrion, Mrna Processing, Mrna Splicing, Nuclease, Hydrolase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Takeuchi, M. Certo, M. G. Caprara, A. M. Scharenberg, B. L. Stoddard
Optimization Of In Vivo Activity Of A Bifunctional Homing Endonuclease And Maturase Reverses Evolutionary Degradation
Nucleic Acids Res. V. 37 877 2009
PubMed-ID: 19103658 | Reference-DOI: 10.1093/NAR/GKN1007

Molecule 1 - INTRON-ENCODED DNA ENDONUCLEASE I-ANII
	Chains	:	A, D, G
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET SYSTEM
	Expression System Strain	:	BL21(DE3)-RIL+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	Y2 I-ANII (UNP RESIDUES 237-488)
	Gene	:	ANCOB INTRON GENE
	Mutation	:	YES
	Organism Common	:	ASPERGILLUS NIDULANS
	Organism Scientific	:	EMERICELLA NIDULANS
	Organism Taxid	:	162425
	Synonym	:	MRNA MATURASE BI1, COB INTRON PROTEIN, TRUNCATED NON- FUNCTIONAL CYTOCHROME B, DNA ENDONUCLEASE/RNA MATURASE I-ANII

Molecule 2 - 31-MER
	Chains	:	B, E, H
	Engineered	:	YES
	Other Details	:	THE PHYSIOLOGICAL DNA TARGET SITE OF I-ANII IN THE MITOCHONDRIAL APOCYTOCHROME B GENE OF A. NIDULANS
	Synthetic	:	YES

Molecule 3 - 31-MER
	Chains	:	C, F, I
	Engineered	:	YES
	Other Details	:	THE PHYSIOLOGICAL DNA TARGET SITE OF I-ANII IN THE MITOCHONDRIAL APOCYTOCHROME B GENE OF A. NIDULANS
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F
Biological Unit 3 (1x)	:							G	H	I

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:16 , ALA A:147 , HOH A:324 , DT B:19 , HOH B:33 , DA C:16	BINDING SITE FOR RESIDUE CA A 301
2	AC2	SOFTWARE	GLY A:15 , GLU A:148 , HOH A:313 , HOH A:315 , DC B:18 , DC C:17	BINDING SITE FOR RESIDUE CA A 302
3	AC3	SOFTWARE	ASP D:16 , ALA D:147 , DT E:19 , DA F:16 , HOH F:34	BINDING SITE FOR RESIDUE CA D 303
4	AC4	SOFTWARE	GLY D:15 , GLU D:148 , GLN D:171 , HOH D:316 , HOH D:322 , DC E:18 , DC F:17	BINDING SITE FOR RESIDUE CA D 304
5	AC5	SOFTWARE	ASP G:16 , ALA G:147 , DT H:19 , DA I:16 , HOH I:33	BINDING SITE FOR RESIDUE CA G 305
6	AC6	SOFTWARE	GLY G:15 , GLU G:148 , GLN G:171 , HOH G:312 , DC H:18 , DC I:17 , HOH I:34	BINDING SITE FOR RESIDUE CA G 306

(no "SS Bond" information available for 3EH8)

(no "Cis Peptide Bond" information available for 3EH8)

(no "SAP(SNP)/Variant" information available for 3EH8)

(no "PROSITE Motif" information available for 3EH8)

(no "Exon" information available for 3EH8)

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:254
 aligned with ANI1_EMEND | P03880 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:254
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    
           ANI1_EMEND   235 AGDLTYAYLVGLFEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKKILGIGIVSFRKINEIEMVALRIRDKNHLKSFILPIFEKYPMFSNKQYDYLRFRNALLSGIISLEDLPDYTRSDEPLNSIESIINTSYFSAWLVGFIEAEGCFSVYKLNKDDDYLIASFDIAQRDGDILISAIRKYLSFTTKVYLDKTNCSKLKVTSVRSVENIIKFLQNAPVKLLGNKKLQYLLWLKQLRKISRYSEKIKIPSNY 488
               SCOP domains d3eh8a1 A:1-125 automated matches                                                                                            d3eh8a2 A:126-254 automated matches                                                                                               SCOP domains
               CATH domains 3eh8A01 A:1-119 Homing endonucleases                                                                                   3eh8A02 A:120-254 Homing endonucleases                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhheeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhh...........hhhhhhh..hhhhhhhhhhhhhheeeeee.......eeeeeeeeee.hhhhhhhhhhhh......ee....eeeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eh8 A   1 GSDLTYAYLVGLYEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKKILGIGIVSFRKRNEIEMVALRIRDKNHLKSKILPIFEKYPMFSNKQYDYLRFRNALLSGIIYLEDLPDYTRSDEPLNSIESIINTSYFSAWLVGFIEAEGCFSVYKLNKDDDYLIASFDIAQRDGDILISAIRKYLSFTTKVYLDKTNCSKLKVTSVRSVENIIKFLQNAPVKLLGNKKLQYKLWLKQLRKISRYSEKIKIPSNY 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:DNA  Length:31
                                                               
                 3eh8 B   1 GCGCGCTGAGGAGGTTTCTCTGTAAAGCGCA  31
                                    10        20        30

Chain C from PDB  Type:DNA  Length:31
                                                               
                 3eh8 C   1 GCGCTTTACAGAGAAACCTCCTCAGCGCGCT  31
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:254
 aligned with ANI1_EMEND | P03880 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:254
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    
           ANI1_EMEND   235 AGDLTYAYLVGLFEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKKILGIGIVSFRKINEIEMVALRIRDKNHLKSFILPIFEKYPMFSNKQYDYLRFRNALLSGIISLEDLPDYTRSDEPLNSIESIINTSYFSAWLVGFIEAEGCFSVYKLNKDDDYLIASFDIAQRDGDILISAIRKYLSFTTKVYLDKTNCSKLKVTSVRSVENIIKFLQNAPVKLLGNKKLQYLLWLKQLRKISRYSEKIKIPSNY 488
               SCOP domains d3eh8d1 D:1-125 automated matches                                                                                            d3eh8d2 D:126-254 automated matches                                                                                               SCOP domains
               CATH domains 3eh8D01 D:1-119 Homing endonucleases                                                                                   3eh8D02 D:120-254 Homing endonucleases                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhheeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..................hhhhhhh..hhhhhhhhhhhhhheeeeee.......eeeeeeeeee.hhhhhhhhhhhh......ee....eeeeee.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eh8 D   1 GSDLTYAYLVGLYEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKKILGIGIVSFRKRNEIEMVALRIRDKNHLKSKILPIFEKYPMFSNKQYDYLRFRNALLSGIIYLEDLPDYTRSDEPLNSIESIINTSYFSAWLVGFIEAEGCFSVYKLNKDDDYLIASFDIAQRDGDILISAIRKYLSFTTKVYLDKTNCSKLKVTSVRSVENIIKFLQNAPVKLLGNKKLQYKLWLKQLRKISRYSEKIKIPSNY 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain E from PDB  Type:DNA  Length:31
                                                               
                 3eh8 E   1 GCGCGCTGAGGAGGTTTCTCTGTAAAGCGCA  31
                                    10        20        30

Chain F from PDB  Type:DNA  Length:31
                                                               
                 3eh8 F   1 GCGCTTTACAGAGAAACCTCCTCAGCGCGCT  31
                                    10        20        30

Chain G from PDB  Type:PROTEIN  Length:254
 aligned with ANI1_EMEND | P03880 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:254
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    
           ANI1_EMEND   235 AGDLTYAYLVGLFEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKKILGIGIVSFRKINEIEMVALRIRDKNHLKSFILPIFEKYPMFSNKQYDYLRFRNALLSGIISLEDLPDYTRSDEPLNSIESIINTSYFSAWLVGFIEAEGCFSVYKLNKDDDYLIASFDIAQRDGDILISAIRKYLSFTTKVYLDKTNCSKLKVTSVRSVENIIKFLQNAPVKLLGNKKLQYLLWLKQLRKISRYSEKIKIPSNY 488
               SCOP domains d3eh8g1 G:1-125 automated matches                                                                                            d3eh8g2 G:126-254 automated matches                                                                                               SCOP domains
               CATH domains 3eh8G01 G:1-119 Homing endonucleases                                                                                   3eh8G02 G:120-254 Homing endonucleases                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhheeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhh.....eeee..eeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhh...........hhhhhhh..hhhhhhhhhhhhhheeeeee.......eeeeeeeeee.hhhhhhhhhhhh......ee....eeeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eh8 G   1 GSDLTYAYLVGLYEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKKILGIGIVSFRKRNEIEMVALRIRDKNHLKSKILPIFEKYPMFSNKQYDYLRFRNALLSGIIYLEDLPDYTRSDEPLNSIESIINTSYFSAWLVGFIEAEGCFSVYKLNKDDDYLIASFDIAQRDGDILISAIRKYLSFTTKVYLDKTNCSKLKVTSVRSVENIIKFLQNAPVKLLGNKKLQYKLWLKQLRKISRYSEKIKIPSNY 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain H from PDB  Type:DNA  Length:31
                                                               
                 3eh8 H   1 GCGCGCTGAGGAGGTTTCTCTGTAAAGCGCA  31
                                    10        20        30

Chain I from PDB  Type:DNA  Length:31
                                                               
                 3eh8 I   1 GCGCTTTACAGAGAAACCTCCTCAGCGCGCT  31
                                    10        20        30

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Homing endonuclease-like (42)

Superfamily: Homing endonucleases (38)

Family: Group I mobile intron endonuclease (29)

Protein domain: automated matches (12)

Emericella nidulans [TaxId: 162425] (1)

1a	d3eh8a1	A:1-125
1b	d3eh8a2	A:126-254
1c	d3eh8d1	D:1-125
1d	d3eh8d2	D:126-254
1e	d3eh8g1	G:1-125
1f	d3eh8g2	G:126-254

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Endonuclease I-creI (41)

Homologous Superfamily: Homing endonucleases (40)

Aspergillus nidulans (Emericella nidulans) (2)

1a	3eh8A02	A:120-254
1b	3eh8D02	D:120-254
1c	3eh8G02	G:120-254
1d	3eh8A01	A:1-119
1e	3eh8D01	D:1-119
1f	3eh8G01	G:1-119

(no "Pfam Domain" information available for 3EH8)

Asymmetric Unit(hide GO term definitions)

Chain A,D,G (ANI1_EMEND | P03880)

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.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006314	intron homing	Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3eh8)

Biological Units
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Access by PDB/NDB ID
	3eh8
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	ANI1_EMEND \| P03880
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	3.1.-.-
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	ANI1_EMEND \| P03880
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	ANI1_EMEND \| P03880	:	1p8k 2qoj

(no "Related Entries Specified in the PDB File" available for 3EH8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

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