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Title :   NMR STRUCTURE OF THE NALP1 PYRIN DOMAIN (PYD)

Authors :   S. Hiller, A. Kohl, F. Fiorito, T. Herrmann, G. Wider, J. Tschopp, M. G. Grutter, K. Wuthrich

Date :   12 Jun 03 (Deposition) - 07 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   5 Alpha-Helix Bundle, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hiller, A. Kohl, F. Fiorito, T. Herrmann, G. Wider, J. Tschopp, M. G. Grutter, K. Wuthrich
Nmr Structure Of The Apoptosis- And Inflammation-Related Nalp1 Pyrin Domain
Structure V. 11 1199 2003
PubMed-ID: 14527388 | Reference-DOI: 10.1016/J.STR.2003.08.009
(for further references see the PDB file header)

Molecule 1 - NACHT-, LRR- AND PYD-CONTAINING PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B+
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PYRIN DOMAIN (PYD)
	Gene	:	NALP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	RESIDUES 1-56 CORRESPOND TO THE FUSED IMMUNOGLOBULIN G BINDING PROTEIN G (SWS P06654, RESIDUES 228-282)
	Synonym	:	DEATH EFFECTOR FILAMENT-FORMING CED-4-LIKE APOPTOSIS PROTEIN, NUCLEOTIDE-BINDING DOMAIN AND CASPASE RECRUITMENT DOMAIN, CASPASE RECRUITMENT DOMAIN PROTEIN 7


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1PN5)

(no "Site" information available for 1PN5)

(no "SS Bond" information available for 1PN5)

(no "Cis Peptide Bond" information available for 1PN5)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069901	M	77	T	NLRP1_HUMAN	Disease (MSPC)	397514692	A	M	135	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAPIN	PS50824	DAPIN domain profile.	NLRP1_HUMAN	1-92	1	A:59-150

(no "Exon" information available for 1PN5)

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
	(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:93
 aligned with NLRP1_HUMAN | Q9C000 from UniProtKB/Swiss-Prot  Length:1473

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
          NLRP1_HUMAN     1 MAGGAWGRLACYLEFLKKEELKEFQLLLANKAHSRSSSGETPAQPEKTSGMEVASYLVAQYGEQRAWDLALHTWEQMGLRSLCAQAQEGAGHS  93
               SCOP domains d1pn5a1 A:59-151 NALP1                                                                        SCOP domains
               CATH domains 1pn5A00 A:59-151 Death Domain, Fas                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh....hhhhhhhhhhhhh....................hhhhhhhhh...hhhhhhhhhhhhhh...hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------T---------------- SAPs(SNPs)
                    PROSITE DAPIN  PDB: A:59-150 UniProt: 1-92                                                          - PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1pn5 A  59 MAGGAWGRLACYLEFLKKEELKEFQLLLANKAHSRSSSGETPAQPEKTSGMEVASYLVAQYGEQRAWDLALHTWEQMGLRSLCAQAQEGAGHS 151
                                    68        78        88        98       108       118       128       138       148

Chain A from PDB  Type:PROTEIN  Length:93
 aligned with SPG1_STRSG | P06654 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:141
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           SPG1_STRSG    11 LRKSAFGLASVSAAFLVGSTVFAVDSPIEDTPIIRNGGELTNLLGNSETTLALRNEESATADLTAAAVADTVAAAAAENAGAAAWEAAAAADALAKAKADALKEFNKYGVSDYYKNLINNAKTVEGIKDLQAQVVESAKKA 151
               SCOP domains d1pn5a1 A:59-151           NAL   P1                                                                                                           SCOP domains
               CATH domains 1pn5A00 A:59-151           Dea   th    Domain, Fas                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh....----------hhh---hh---hhhhhhhh....................--hhhhhhhhh...hhhhhhhh-------------hhhhhh..-----------------.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------T--------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pn5 A  59 MAGGAWGRLACYLEFLK----------KEE---LK---EFQLLLANKAHSRSSSGETPAQPEKTSG--MEVASYLVAQYGEQRAWDLA-------------LHTWEQMG-----------------LRSLCAQAQEGAGHS 151
                                    68      |  -       |78   ||   82        92       102     | 110       120       | -         - |      |-         -      |140       150 
                                           75         76 |  79|  81                        108  |                128           129    136               137              
                                                        78   80                               109

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DEATH domain (37)

Superfamily: DEATH domain (37)

Family: Pyrin domain, PYD (3)

Protein domain: NALP1 (1)

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

d1pn5a1

A:59-151

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Death Domain, Fas (26)

Homologous Superfamily: Death Domain, Fas (26)

Human (Homo sapiens) (20)

1pn5A00

A:59-151

(no "Pfam Domain" information available for 1PN5)

NMR Structure(hide GO term definitions)

Chain A (SPG1_STRSG | P06654)

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 A (NLRP1_HUMAN | Q9C000)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008656	cysteine-type endopeptidase activator activity involved in apoptotic process	Increases the rate of proteolysis catalyzed by a cysteine-type endopeptidase involved in the apoptotic process.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
biological process
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	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:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0051402	neuron apoptotic process	Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
	GO:0050718	positive regulation of interleukin-1 beta secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:0032495	response to muramyl dipeptide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.
cellular component
	GO:0072558	NLRP1 inflammasome complex	A protein complex that consists of two components, NLRP1 (NALP1) and caspase-1 or caspase-5. The exact mechanisms of NLRP1 activation remain obscure, but potassium ion efflux appears to be essential.
	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:0061702	inflammasome complex	A cytosolic protein complex that is capable of activating caspase-1.
	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: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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