3BSU - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HYBRID-BINDING DOMAIN OF HUMAN RNASE H1 IN COMPLEX WITH 12-MER RNA/DNA

Authors :   M. Nowotny, S. M. Cerritelli, R. Ghirlando, S. A. Gaidamakov, R. J. Crouch, W. Yang

Date :   26 Dec 07 (Deposition) - 25 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Rnase H, Rna/Dna Hybrid, Dsrna, Hydrolase/Rna/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nowotny, S. M. Cerritelli, R. Ghirlando, S. A. Gaidamakov, R. J. Crouch, W. Yang
Specific Recognition Of Rna/Dna Hybrid And Enhancement Of Human Rnase H1 Activity By Hbd.
Embo J. V. 27 1172 2008
PubMed-ID: 18337749 | Reference-DOI: 10.1038/EMBOJ.2008.44
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE H1
	Chains	:	A, B, C, F, G, H
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15
	Expression System Strain	:	BL21 ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	RNASEH1, RNH1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNASE H1; RIBONUCLEASE H TYPE II

*Molecule 2 - RNA (5'-R(GPAPCPAPCPCPUPGPAPUPUPC)- 3')*
	Chains	:	D, I
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(DGPDAPDAPDTPDCPDAPDGPDGP(5IU) PDGPDTPDC)-3')*
	Chains	:	E, J
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J
Biological Unit 1 (1x)	:	A	B	C	D	E
Biological Unit 2 (1x)	:						F	G	H	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	5IU	2	Mod. Nucleotide	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	5IU	1	Mod. Nucleotide	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	5IU	1	Mod. Nucleotide	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE C:40 , LEU C:41 , GLU C:45	BINDING SITE FOR RESIDUE MG C 502

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

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

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

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

Asymmetric Unit (2, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000315212	1a	ENSE00001253796	chr2:3606206-3605723	484	RNH1_HUMAN	1-43	43	6	A:26-43 (gaps) B:26-43 (gaps) C:27-43 F:25-43 (gaps) G:24-43 (gaps) H:26-43 (gaps)	35 35 17 36 23 35
1.3	ENST00000315212	3	ENSE00001764472	chr2:3604494-3604379	116	RNH1_HUMAN	43-82	40	6	A:43-73 B:43-73 C:43-74 F:43-73 G:43-73 H:43-72	31 31 32 31 31 30
1.4	ENST00000315212	4	ENSE00001613471	chr2:3599898-3599734	165	RNH1_HUMAN	82-137	56	0	-	-
1.5b	ENST00000315212	5b	ENSE00001792991	chr2:3598062-3597963	100	RNH1_HUMAN	137-170	34	0	-	-
1.6	ENST00000315212	6	ENSE00001703361	chr2:3596702-3596648	55	RNH1_HUMAN	170-188	19	0	-	-
1.7	ENST00000315212	7	ENSE00001702047	chr2:3596314-3596230	85	RNH1_HUMAN	189-217	29	0	-	-
1.8	ENST00000315212	8	ENSE00001759845	chr2:3595645-3595521	125	RNH1_HUMAN	217-258	42	0	-	-
1.9a	ENST00000315212	9a	ENSE00001253775	chr2:3593461-3592705	757	RNH1_HUMAN	259-286	28	0	-	-

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:48
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:65
                                    18        28        38        48        58        68     
            RNH1_HUMAN    9 HRVALAALPCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
               SCOP domains d                 3bsua_ A: automated matches                     SCOP domains
               CATH domains 3                 bsuA00 A:26-73 Ribonuclease Hi; Chain A         CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------------.eeeeee....eee.hhhhhhhhhh.....eeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:26-43 (gaps)     ------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: A:43-73          Transcript 1 (2)
                  3bsu A 26 H-----------------MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
                            |        -        28        38        48        58        68     
                            |                27                                              
                           26

Chain B from PDB  Type:PROTEIN  Length:48
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:65
                                    18        28        38        48        58        68     
            RNH1_HUMAN    9 HRVALAALPCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
               SCOP domains d                 3bsub_ B: automated matches                     SCOP domains
               CATH domains 3                 bsuB00 B:26-73 Ribonuclease Hi; Chain A         CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------------.eeeeee....eee.hhhhhhhhhh.....eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:26-43 (gaps)     ------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: B:43-73          Transcript 1 (2)
                  3bsu B 26 H-----------------MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
                            |        -        28        38        48        58        68     
                           26                27

Chain C from PDB  Type:PROTEIN  Length:48
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:48
                                    36        46        56        66        
            RNH1_HUMAN   27 MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRKS 74
               SCOP domains d3bsuc_ C: automated matches                     SCOP domains
               CATH domains 3bsuC00 C:27-74 Ribonuclease Hi; Chain A         CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eee.hhhhhhhhhh.....eeeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a        ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.3  PDB: C:43-74           Transcript 1 (2)
                  3bsu C 27 MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRKS 74
                                    36        46        56        66

Chain D from PDB  Type:RNA  Length:12
                                           
                  3bsu D  1 GACACCUGAUUC 12
                                    10

Chain E from PDB  Type:DNA  Length:12
                                           
                  3bsu E  1 GAATCAGGuGTC 12
                                    10  
                                    9-5IU

Chain F from PDB  Type:PROTEIN  Length:49
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:66
                                    17        27        37        47        57        67      
            RNH1_HUMAN    8 AHRVALAALPCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
               SCOP domains d3                 bsuf_ F: automated matches                      SCOP domains
               CATH domains 3b                 suF00 F:25-73 Ribonuclease Hi; Chain A          CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------------.eeeeee....eee.hhhhhhhhhh.....eeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: F:25-43 (gaps)      ------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.3  PDB: F:43-73          Transcript 1 (2)
                  3bsu F 25 SH-----------------MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
                             |       -        27        37        47        57        67      
                            26                27

Chain G from PDB  Type:PROTEIN  Length:50
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:53
                                    30        40        50        60        70   
            RNH1_HUMAN   21 GSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
               SCOP domains d3b   sug_ G: automated matches                       SCOP domains
               CATH domains 3bs   uG00 G:24-73 Ribonuclease Hi; Chain A           CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...---.eeeeee....eee.hhhhhhhhhh.....eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a UniProt: 1-43------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.3  PDB: G:43-73          Transcript 1 (2)
                  3bsu G 24 GSH---MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRK 73
                              |   | 30        40        50        60        70   
                             26  27

Chain H from PDB  Type:PROTEIN  Length:47
 aligned with RNH1_HUMAN | O60930 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:64
                                    18        28        38        48        58        68    
            RNH1_HUMAN    9 HRVALAALPCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVR 72
               SCOP domains d                 3bsuh_ H: automated matches                    SCOP domains
               CATH domains 3                 bsuH00 H:26-72 Ribonuclease Hi; Chain A        CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----------------.eeeeee....eee.hhhhhhhhhh.....eeeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: H:26-43 (gaps)     ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: H:43-72         Transcript 1 (2)
                  3bsu H 26 H-----------------MFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVR 72
                            |        -        28        38        48        58        68    
                           26                27

Chain I from PDB  Type:RNA  Length:12
                                           
                  3bsu I  1 GACACCUGAUUC 12
                                    10

Chain J from PDB  Type:DNA  Length:12
                                           
                  3bsu J  1 GAATCAGGuGTC 12
                                    10  
                                    9-5IU

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: MbtH/L9 domain-like (48)

Superfamily: L9 N-domain-like (45)

Family: automated matches (1)

Protein domain: automated matches (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d3bsua_	A:
1b	d3bsub_	B:
1c	d3bsuc_	C:
1d	d3bsuf_	F:
1e	d3bsug_	G:
1f	d3bsuh_	H:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Ribonuclease HI; Chain A (10)

Homologous Superfamily: Ribonuclease Hi; Chain A (2)

Human (Homo sapiens) (1)

1a	3bsuA00	A:26-73
1b	3bsuB00	B:26-73
1c	3bsuC00	C:27-74
1d	3bsuF00	F:25-73
1e	3bsuH00	H:26-72
1f	3bsuG00	G:24-73

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,F,G,H (RNH1_HUMAN | O60930)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0043137	DNA replication, removal of RNA primer	Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
	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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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