3UN9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF AN IMMUNE RECEPTOR

Authors :   M. Hong, S. I. Yoon, I. A. Wilson

Date :   15 Nov 11 (Deposition) - 28 Mar 12 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)

Keywords :   Leucine Rich Repeat (Lrr), Antiviral Signaling, Mavs, Traf6, Ikk, Uqcrc2, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hong, S. I. Yoon, I. A. Wilson
Structure And Functional Characterization Of The Rna-Bindin Element Of The Nlrx1 Innate Immune Modulator.
Immunity V. 36 337 2012
PubMed-ID: 22386589 | Reference-DOI: 10.1016/J.IMMUNI.2011.12.018

Molecule 1 - NLR FAMILY MEMBER X1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HI-5
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PLASMID
	Expression System Taxid	:	7111
	Fragment	:	RNA-BINDING ELEMENT (UNP RESIDUES 629-975)
	Gene	:	NLRX1, NOD26, NOD5, NOD9
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CATERPILLER PROTEIN 11.3, CLR11.3, NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 26, NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 5, NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 9

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	PT	4	Ligand/Ion	PLATINUM (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	PT	-1	Ligand/Ion	PLATINUM (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:816	BINDING SITE FOR RESIDUE PT A 1001
2	AC2	SOFTWARE	HIS B:816	BINDING SITE FOR RESIDUE PT B 1001
3	AC3	SOFTWARE	HIS C:816	BINDING SITE FOR RESIDUE PT C 1001

(no "SS Bond" information available for 3UN9)

(no "Cis Peptide Bond" information available for 3UN9)

Asymmetric Unit (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034616	A	793	E	NLRX1_HUMAN	Polymorphism	4245191	A/B/C	A	793	E
2	UniProt	VAR_034617	A	843	S	NLRX1_HUMAN	Polymorphism	35500631	A/B/C	A	843	S

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

Biological Unit 1 (2, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034616	A	793	E	NLRX1_HUMAN	Polymorphism	4245191	A/B/C	A	793	E
2	UniProt	VAR_034617	A	843	S	NLRX1_HUMAN	Polymorphism	35500631	A/B/C	A	843	S

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

(no "PROSITE Motif" information available for 3UN9)

(no "Exon" information available for 3UN9)

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:294
 aligned with NLRX1_HUMAN | Q86UT6 from UniProtKB/Swiss-Prot  Length:975

    Alignment length:304
                                   676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966    
          NLRX1_HUMAN   667 RQVLPPSELLDHLFFHYEFQNQRFSAEVLSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELSSEGRQVLRDLGGAAEGGARVVVSLTEGTAVSEYWSVILSEVQRNLNSWDRARVQRHLELLLRDLEDSRGATLNPWRKAQLLRVEGEVRALLEQL 970
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhheeeee......hhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhh....eee......hhhhhhhhhhh------..eee....----.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------E-------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3un9 A 667 RQVLPPSELLDHLFFHYEFQNQRFSAEVLSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELSSEGRQVLRDL------GARVVVSLT----VSEYWSVILSEVQRNLNSWDRARVQRHLELLLRDLEDSRGATLNPWRKAQLLRVEGEVRALLEQL 970
                                   676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      |896    |  906       916       926       936       946       956       966    
                                                                                                                                                                                                                                                     886    893     901  906

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with NLRX1_HUMAN | Q86UT6 from UniProtKB/Swiss-Prot  Length:975

    Alignment length:304
                                   676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966    
          NLRX1_HUMAN   667 RQVLPPSELLDHLFFHYEFQNQRFSAEVLSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELSSEGRQVLRDLGGAAEGGARVVVSLTEGTAVSEYWSVILSEVQRNLNSWDRARVQRHLELLLRDLEDSRGATLNPWRKAQLLRVEGEVRALLEQL 970
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhheeeee......hhhhhhhhhhhhhh......eee......hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhh.....eee......hhhhhhhhhhh------..eee....----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------E-------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3un9 B 667 RQVLPPSELLDHLFFHYEFQNQRFSAEVLSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELSSEGRQVLRDL------GARVVVSLT----VSEYWSVILSEVQRNLNSWDRARVQRHLELLLRDLEDSRGATLNPWRKAQLLRVEGEVRALLEQL 970
                                   676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      |896    |  906       916       926       936       946       956       966    
                                                                                                                                                                                                                                                     886    893     901  906

Chain C from PDB  Type:PROTEIN  Length:279
 aligned with NLRX1_HUMAN | Q86UT6 from UniProtKB/Swiss-Prot  Length:975

    Alignment length:301
                                   678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968 
          NLRX1_HUMAN   669 VLPPSELLDHLFFHYEFQNQRFSAEVLSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELSSEGRQVLRDLGGAAEGGARVVVSLTEGTAVSEYWSVILSEVQRNLNSWDRARVQRHLELLLRDLEDSRGATLNPWRKAQLLRVEGEVRALLEQ 969
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh......eee......hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhh.....eee......hhhhhhhhhhh------..eee....----..hhhhhhh....----------..hhhhhhhhhhhhhhh..--...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------E-------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3un9 C 669 VLPPSELLDHLFFHYEFQNQRFSAEVLSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELSSEGRQVLRDL------GARVVVSLT----VSEYWSVILSEVQ----------VQRHLELLLRDLEDSRGAT--PWRKAQLLRVEGEVRALLEQ 969
                                   678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       | -    |  898  |    908       918         -|      938        |- |     958       968 
                                                                                                                                                                                                                                                   886    893     901  906         918        929               947  |                   
                                                                                                                                                                                                                                                                                                                   950

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 '\|'

(no "SCOP Domain" information available for 3UN9)

(no "CATH Domain" information available for 3UN9)

(no "Pfam Domain" information available for 3UN9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NLRX1_HUMAN | Q86UT6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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).
biological process
	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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB signaling	Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.
	GO:0039536	negative regulation of RIG-I signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0045824	negative regulation of innate immune response	Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.
	GO:0032688	negative regulation of interferon-beta production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta production.
	GO:0032715	negative regulation of interleukin-6 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
	GO:0032480	negative regulation of type I interferon production	Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 6)

PROSITE Motifs (0, 0)

Exons (0, 0)

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