1IBX - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR STRUCTURE OF DFF40 AND DFF45 N-TERMINAL DOMAIN COMPLEX

Authors :   P. Zhou, A. A. Lugovskoy, J. S. Mccarty, P. Li, G. Wagner

Date :   29 Mar 01 (Deposition) - 02 May 01 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)

Keywords :   Dff40, Dff45, Protein-Protein Complex, Cide, Cide Domain Complex, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Zhou, A. A. Lugovskoy, J. S. Mccarty, P. Li, G. Wagner
Solution Structure Of Dff40 And Dff45 N-Terminal Domain Complex And Mutual Chaperone Activity Of Dff40 And Dff45.
Proc. Natl. Acad. Sci. Usa V. 98 6051 2001
PubMed-ID: 11371636 | Reference-DOI: 10.1073/PNAS.111145098
(for further references see the PDB file header)

Molecule 1 - DNA FRAGMENTATION FACTOR 40
	Chains	:	A
	EC Number	:	3.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-30A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN (CIDE DOMAIN)
	Gene	:	DFF40
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DFF40, CASPASE-ACTIVATED DNASE, CASPASE-ACTIVATED NUCLEASE

Molecule 2 - CHIMERA OF IGG BINDING PROTEIN G AND DNA FRAGMENTATION FACTOR 45
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-30A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	B1 DOMAIN OF PROTEIN G FUSED WITH N-TERMINAL DOMAIN (CIDE DOMAIN) OF DFF45
	Gene	:	DFF45
	Mutation	:	YES
	Organism Common	:	, HUMAN
	Organism Scientific	:	STREPTOCOCCUS SP., HOMO SAPIENS
	Organism Taxid	:	1306,9606
	Strain	:	,
	Synonym	:	DFF45, INHIBITOR OF CAD


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1IBX)

(no "SS Bond" information available for 1IBX)

(no "Cis Peptide Bond" information available for 1IBX)

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

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CIDE_N	PS51135	CIDE-N domain profile.	DFFB_HUMAN	4-80	1	A:4-80
1	CIDE_N	PS51135	CIDE-N domain profile.	DFFA_HUMAN	17-96	1	B:17-96

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000378209	1a	ENSE00002162748	chr1:3773845-3774281	437	DFFB_HUMAN	1-38	38	1	A:1-38	38
1.2a	ENST00000378209	2a	ENSE00001762006	chr1:3775282-3775408	127	DFFB_HUMAN	39-81	43	1	A:39-81	43
1.4d	ENST00000378209	4d	ENSE00001657268	chr1:3782376-3782564	189	DFFB_HUMAN	81-144	64	1	A:81-81	1
1.6b	ENST00000378209	6b	ENSE00001701315	chr1:3784538-3784617	80	DFFB_HUMAN	144-170	27	0	-	-
1.7	ENST00000378209	7	ENSE00001592455	chr1:3786169-3786339	171	DFFB_HUMAN	171-227	57	0	-	-
1.8b	ENST00000378209	8b	ENSE00001719401	chr1:3789036-3789136	101	DFFB_HUMAN	228-261	34	0	-	-
1.10d	ENST00000378209	10d	ENSE00001476660	chr1:3800071-3801993	1923	DFFB_HUMAN	261-338	78	0	-	-

NMR Structure

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:81
 aligned with DFFB_HUMAN | O76075 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:81
                                    10        20        30        40        50        60        70        80 
           DFFB_HUMAN     1 MLQKPKSVKLRALRSPRKFGVAGRSCQEVLRKGCLRFQLPERGSRLCLYEDGTELTEDYFPSVPDNAELVLLTLGQAWQGY  81
               SCOP domains d1ibxa_ A: Caspase-activated DNase (CAD), DFF40, N-terminal domain                SCOP domains
               CATH domains 1ibxA00 A:1-81  [code=3.10.20.10, no name defined]                                CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.............hhhhhhhhhhhhh.......eeee....................eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CIDE_N  PDB: A:4-80 UniProt: 4-80                                            - PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-38 UniProt: 1-38  Exon 1.2a  PDB: A:39-81 UniProt: 39-81      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------1 Transcript 1 (2)
                 1ibx A   1 MLQKPKSVKLRALRSPRKFGVAGRSCQEVLRKGCLRFQLPERGSRLCLYEDGTELTEDYFPSVPDNAELVLLTLGQAWQGH  81
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with DFFA_HUMAN | O00273 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:89
                                    21        31        41        51        61        71        81        91         
           DFFA_HUMAN    12 SGEIRTLKPCLLRRNYSREQHGVAASCLEDLRSKACDILAIDKSLTPVTLVLAEDGTIVDDDDYFLCLPSNTKFVALASNEKWAYNNSD 100
               SCOP domains d1ibxb_ B: Inhibitor of caspase-activated DNase (ICAD), DFF45, N-terminal domain          SCOP domains
               CATH domains 1ibxB00 B:12-100  [code=3.10.20.10, no name defined]                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhh........eeee........hhhhhhhh.....eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----CIDE_N  PDB: B:17-96 UniProt: 17-96                                             ---- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1ibx B  12 SGEIRTLKPCLLRRNYSREQHGVAASCLEDLRSKACDILAIDKSLTPVTLVLAEDGTIVDDDDYFLCLPSNTKFVALASNEKWAYNNSD 100
                                    21        31        41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with SPG2_STRSG | P19909 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:107
                                   323       333       343       353       363       373       383       393       403       413       
           SPG2_STRSG   314 KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDAT 420
               SCOP domains d1ibx  b_ B: Inhibit  or of caspase-activate    d D Nase   (ICAD), DFF45,    N-terminal domain              SCOP domains
               CATH domains 1ibxB  00 B:12-100    [code=3.10.20.10, no n    ame  def  ined]                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--.............--........hhhhhhhhhhhhhh----...-....--.eeee........hh---hhhhhh.....eeee....----........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1ibx B  12 SGEIR--TLKPCLLRRNYSR--EQHGVAASCLEDLRSKACDILA----IDK-SLTP--VTLVLAEDGTIVDDD---DYFLCLPSNTKFVALASNE----KWAYNNSD 100
                                |  |19        29  |     37        47   |    53| |  |  60        70  |   | 77        87    |   93       
                               16 17          29 30                   51   52 | | 58 59            73  74                92   93       
                                                                             54 |                                                      
                                                                               55

Legend:		→ Mismatch	(orange background)
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	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 '\|'

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.10, no name defined] (72)

Human (Homo sapiens) (4)

1a	1ibxA00	A:1-81
1b	1ibxB00	B:12-100

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

NMR Structure(hide GO term definitions)

Chain A (DFFB_HUMAN | O76075)

molecular function
	GO:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0006309	apoptotic DNA fragmentation	The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
	GO:0030263	apoptotic chromosome condensation	The compaction of chromatin during apoptosis.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Chain B (SPG2_STRSG | P19909)

molecular function
	GO:0019864	IgG binding	Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B (DFFA_HUMAN | O00273)

molecular function
	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).
biological process
	GO:0006309	apoptotic DNA fragmentation	The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:1902511	negative regulation of apoptotic DNA fragmentation	Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation.
	GO:1900118	negative regulation of execution phase of apoptosis	Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0070242	thymocyte apoptotic process	Any apoptotic process in a thymocyte, an immature T cell located in the thymus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

NMR Structure
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