1RF3 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURALLY DISTINCT RECOGNITION MOTIFS IN LYMPHOTOXIN-B RECEPTOR AND CD40 FOR TRAF-MEDIATED SIGNALING

Authors :   C. Li, P. S. Norris, C. Z. Ni, M. L. Havert, E. M. Chiong, B. R. Tran, E. Cabezas, G. Cheng, J. C. Reed, A. C. Satterthwait, C. F. Ware, K. R. El

Date :   07 Nov 03 (Deposition) - 06 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Cd40, Nf-Kb Signaling, Ltbr, Tnf Receptor, Traf3 Crystallography, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Li, P. S. Norris, C. Z. Ni, M. L. Havert, E. M. Chiong, B. R. Tran, E. Cabezas, J. C. Reed, A. C. Satterthwait, C. F. Ware, K. R. Ely
Structurally Distinct Recognition Motifs In Lymphotoxin-Beta Receptor And Cd40 For Tumor Necrosis Factor Receptor-Associated Factor (Traf)-Mediated Signaling.
J. Biol. Chem. V. 278 50523 2003
PubMed-ID: 14517219 | Reference-DOI: 10.1074/JBC.M309381200
(for further references see the PDB file header)

Molecule 1 - TNF RECEPTOR ASSOCIATED FACTOR 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RECOGNITION MOTIF (RESIDUES 377-568)
	Gene	:	TRAF3 OR CRAF1 OR CAP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CD40 RECEPTOR ASSOCIATED FACTOR 1, CRAF1, CD40 BINDING PROTEIN, CD40BP, LMP1 ASSOCIATED PROTEIN, LAP1, CAP-1

Molecule 2 - 24-RESIDUE PEPTIDE FROM LYMPHOTOXIN-B RECEPTOR
	Chains	:	B
	Engineered	:	YES
	Fragment	:	RECOGNITION MOTIF (RESIDUES 385-408)
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED, THE SEQUENCE OF THE PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1RF3)

(no "Site" information available for 1RF3)

(no "SS Bond" information available for 1RF3)

Asymmetric Unit

No.	Residues
1	Trp A:424	-	Pro A:425

(no "SAP(SNP)/Variant" information available for 1RF3)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MATH	PS50144	MATH/TRAF domain profile.	TRAF3_HUMAN	415-560	1	A:351-496

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MATH	PS50144	MATH/TRAF domain profile.	TRAF3_HUMAN	415-560	3	A:351-496

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000228918	1	ENSE00001216440	chr12:6493334-6493620	287	TNR3_HUMAN	1-32	32	0	-	-
1.2	ENST00000228918	2	ENSE00000714969	chr12:6493754-6493850	97	TNR3_HUMAN	33-65	33	0	-	-
1.3	ENST00000228918	3	ENSE00000714970	chr12:6494188-6494313	126	TNR3_HUMAN	65-107	43	0	-	-
1.4	ENST00000228918	4	ENSE00000714971	chr12:6494393-6494545	153	TNR3_HUMAN	107-158	52	0	-	-
1.5	ENST00000228918	5	ENSE00000714972	chr12:6495232-6495328	97	TNR3_HUMAN	158-190	33	0	-	-
1.6	ENST00000228918	6	ENSE00000714973	chr12:6495513-6495610	98	TNR3_HUMAN	190-223	34	0	-	-
1.7	ENST00000228918	7	ENSE00000866902	chr12:6497564-6497671	108	TNR3_HUMAN	223-259	37	0	-	-
1.8	ENST00000228918	8	ENSE00001044353	chr12:6497966-6497991	26	TNR3_HUMAN	259-267	9	0	-	-
1.9	ENST00000228918	9	ENSE00000866903	chr12:6499278-6499506	229	TNR3_HUMAN	268-344	77	0	-	-
1.10	ENST00000228918	10	ENSE00000866904	chr12:6499826-6500733	908	TNR3_HUMAN	344-435	92	1	B:385-408	24

2.1	ENST00000392745	1	ENSE00001452921	chr14:103243816-103244012	197	TRAF3_HUMAN	-	0	0	-	-
2.2	ENST00000392745	2	ENSE00001512975	chr14:103296671-103296809	139	TRAF3_HUMAN	-	0	0	-	-
2.3	ENST00000392745	3	ENSE00001026101	chr14:103336522-103336783	262	TRAF3_HUMAN	1-82	82	0	-	-
2.4	ENST00000392745	4	ENSE00000660513	chr14:103338254-103338305	52	TRAF3_HUMAN	82-99	18	0	-	-
2.5	ENST00000392745	5	ENSE00000660514	chr14:103341961-103342065	105	TRAF3_HUMAN	100-134	35	0	-	-
2.6	ENST00000392745	6	ENSE00000660515	chr14:103342695-103342862	168	TRAF3_HUMAN	135-190	56	0	-	-
2.7	ENST00000392745	7	ENSE00000660516	chr14:103352526-103352606	81	TRAF3_HUMAN	191-217	27	0	-	-
2.8	ENST00000392745	8	ENSE00000660517	chr14:103355897-103355971	75	TRAF3_HUMAN	218-242	25	0	-	-
2.9	ENST00000392745	9	ENSE00000660518	chr14:103357662-103357754	93	TRAF3_HUMAN	243-273	31	0	-	-
2.10	ENST00000392745	10	ENSE00000660519	chr14:103363598-103363738	141	TRAF3_HUMAN	274-320	47	0	-	-
2.11	ENST00000392745	11	ENSE00000660520	chr14:103369592-103369766	175	TRAF3_HUMAN	321-379	59	1	A:313-315	3
2.12	ENST00000392745	12	ENSE00001152460	chr14:103371550-103372628	1079	TRAF3_HUMAN	379-568	190	1	A:315-504	190

Asymmetric Unit

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	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:192
 aligned with TRAF3_HUMAN | Q13114 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:192
                                   386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566  
          TRAF3_HUMAN   377 NTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 568
               SCOP domains d1rf3a2 A:313-349 TRAF3              d1rf3a1 A:350-504 TNF receptor associated factor 3 (TRAF3)                                                                                                  SCOP domains
               CATH domains 1rf3A00 A:313-504 Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A                                                                                                        CATH domains
               Pfam domains ---------------------------------------------MATH-1rf3A01 A:358-498                                                                                                                       ------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhh.........ee......ee..eee............eee.....................eee..........ee............................hhhhhhh.......eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------MATH  PDB: A:351-496 UniProt: 415-560                                                                                                             -------- PROSITE
           Transcript 2 (1) 2.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) --Exon 2.12  PDB: A:315-504 UniProt: 379-568                                                                                                                                                     Transcript 2 (2)
                 1rf3 A 313 NTGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTSDLPDP 504
                                   322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502

Chain B from PDB  Type:PROTEIN  Length:24
 aligned with TNR3_HUMAN | P36941 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:24
                                   394       404    
           TNR3_HUMAN   385 PYPIPEEGDPGPPGLSTPHQEDGK 408
               SCOP domains d1rf3b_ B:               SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
               Transcript 1 Exon 1.10  PDB: B:385-40 Transcript 1
                 1rf3 B 385 PYPIPEEGDPGPPGLSTPHQEDGK 408
                                   394       404

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A (23)

Homologous Superfamily: Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A (23)

Human (Homo sapiens) (21)

1rf3A00

A:313-504

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TRAF (11)

Family: MATH (9)

Homo sapiens (Human) (9)

MATH-1rf3A01

A:358-498

Asymmetric Unit(hide GO term definitions)

Chain A (TRAF3_HUMAN | Q13114)

molecular function
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0031996	thioesterase binding	Interacting selectively and non-covalently with any thioesterase enzyme.
	GO:0005164	tumor necrosis factor receptor binding	Interacting selectively and non-covalently with the tumor necrosis factor receptor.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0035666	TRIF-dependent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0008063	Toll signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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: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:0032088	negative regulation of NF-kappaB transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
	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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0001817	regulation of cytokine production	Any process that modulates the frequency, rate, or extent of production of a cytokine.
	GO:0050688	regulation of defense response to virus	Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.
	GO:0032648	regulation of interferon-beta production	Any process that modulates the frequency, rate, or extent of interferon-beta production.
	GO:0030162	regulation of proteolysis	Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0002224	toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0035631	CD40 receptor complex	A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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.

Chain B (TNR3_HUMAN | P36941)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005031	tumor necrosis factor-activated receptor activity	Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological 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:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0043011	myeloid dendritic cell differentiation	The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0032496	response to lipopolysaccharide	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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 1rf3)

	Cis Peptide Bonds
		Trp A:424 - Pro A:425	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1rf3
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	TNR3_HUMAN \| P36941
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	TRAF3_HUMAN \| Q13114
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	TNR3_HUMAN \| P36941	:	4mxw
	TRAF3_HUMAN \| Q13114	:	1flk 1fll 1kzz 1l0a 1zms 2ecy 2gkw

(no "Related Entries Specified in the PDB File" available for 1RF3)

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