3DO7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF A NF-KB P52/RELB/DNA COMPLEX

Authors :   A. Fusco, D. B. Huang, D. Miller, D. Vu, G. Ghosh

Date :   03 Jul 08 (Deposition) - 21 Jul 09 (Release) - 18 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.05

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

Keywords :   Protein-Dna Complex, Nucleus, Activator, Alternative Splicing, Ank Repeat, Chromosomal Rearrangement, Cytoplasm, Disease Mutation, Dna-Binding, Phosphoprotein, Polymorphism, Proto-Oncogene, Transcription, Transcription Regulation, Ubl Conjugation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Fusco, D. B. Huang, D. Miller, D. Vu, G. Ghosh
Nf-Kapppab P52:Relb Heterodimer Uses Different Binding Modes To Recognize Different Kappab Dna
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - AVIAN RETICULOENDOTHELIOSIS VIRAL (V-REL) ONCOGENE RELATED B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	T7 PROMOTER
	Fragment	:	RHR (UNP RESIDUES 88-383)
	Gene	:	RELB
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - NUCLEAR FACTOR NF-KAPPA-B P100 SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	T7 PROMOTER
	Fragment	:	RHR (UNP RESIDUES 37-329)
	Gene	:	NFKB2, LYT10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DNA-BINDING FACTOR KBF2, H2TF1, LYMPHOCYTE TRANSLOCATION CHROMOSOME 10, ONCOGENE LYT-10, LYT10, NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT

*Molecule 3 - 5'- D(DCPDGPDGPDGPDAPDAPDTPDTPDCPDCPDC)-3'**
	Chains	:	C, D, E
	Engineered	:	YES
	Fragment	:	KAPPA B SITE
	Other Details	:	KAPPAB DNA
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:					E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3DO7)

(no "Site" information available for 3DO7)

Asymmetric Unit

No.	Residues
1	A:181	-	A:186
2	B:114	-	B:120

(no "Cis Peptide Bond" information available for 3DO7)

(no "SAP(SNP)/Variant" information available for 3DO7)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	REL_1	PS01204	NF-kappa-B/Rel/dorsal domain signature.	NFKB2_HUMAN	53-59	1	B:53-59
1	REL_1	PS01204	NF-kappa-B/Rel/dorsal domain signature.	RELB_MOUSE	118-124	1	A:118-124
2	REL_2	PS50254	NF-kappa-B/Rel/dorsal domain profile.	RELB_MOUSE	100-277	1	A:100-277

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	REL_1	PS01204	NF-kappa-B/Rel/dorsal domain signature.	NFKB2_HUMAN	53-59	1	B:53-59
1	REL_1	PS01204	NF-kappa-B/Rel/dorsal domain signature.	RELB_MOUSE	118-124	1	A:118-124
2	REL_2	PS50254	NF-kappa-B/Rel/dorsal domain profile.	RELB_MOUSE	100-277	1	A:100-277

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	REL_1	PS01204	NF-kappa-B/Rel/dorsal domain signature.	NFKB2_HUMAN	53-59	0	-
1	REL_1	PS01204	NF-kappa-B/Rel/dorsal domain signature.	RELB_MOUSE	118-124	0	-
2	REL_2	PS50254	NF-kappa-B/Rel/dorsal domain profile.	RELB_MOUSE	100-277	0	-

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000369966	1b	ENSE00001451363	chr10:104154354-104154531	178	NFKB2_HUMAN	-	0	0	-	-
1.2d	ENST00000369966	2d	ENSE00002189547	chr10:104155645-104155737	93	NFKB2_HUMAN	1-7	7	0	-	-
1.3	ENST00000369966	3	ENSE00001377720	chr10:104156010-104156091	82	NFKB2_HUMAN	8-35	28	0	-	-
1.4	ENST00000369966	4	ENSE00000811509	chr10:104156206-104156246	41	NFKB2_HUMAN	35-48	14	1	B:37-48	12
1.5b	ENST00000369966	5b	ENSE00000811510	chr10:104156482-104156580	99	NFKB2_HUMAN	49-81	33	1	B:49-81	33
1.6	ENST00000369966	6	ENSE00000503288	chr10:104156661-104156812	152	NFKB2_HUMAN	82-132	51	1	B:82-132	51
1.7	ENST00000369966	7	ENSE00000811512	chr10:104157059-104157165	107	NFKB2_HUMAN	132-168	37	1	B:132-168	37
1.8	ENST00000369966	8	ENSE00000811513	chr10:104157284-104157442	159	NFKB2_HUMAN	168-221	54	1	B:168-221	54
1.9	ENST00000369966	9	ENSE00000811514	chr10:104157738-104157842	105	NFKB2_HUMAN	221-256	36	1	B:221-256	36
1.10	ENST00000369966	10	ENSE00000811515	chr10:104157969-104158054	86	NFKB2_HUMAN	256-284	29	1	B:256-284	29
1.11	ENST00000369966	11	ENSE00000811516	chr10:104158142-104158280	139	NFKB2_HUMAN	285-331	47	1	B:285-329	45
1.12a	ENST00000369966	12a	ENSE00000503294	chr10:104158496-104158621	126	NFKB2_HUMAN	331-373	43	0	-	-
1.13	ENST00000369966	13	ENSE00000722725	chr10:104159045-104159254	210	NFKB2_HUMAN	373-443	71	0	-	-
1.14	ENST00000369966	14	ENSE00001192756	chr10:104159334-104159475	142	NFKB2_HUMAN	443-490	48	0	-	-
1.15	ENST00000369966	15	ENSE00000722730	chr10:104159837-104159951	115	NFKB2_HUMAN	490-528	39	0	-	-
1.16	ENST00000369966	16	ENSE00000722731	chr10:104160035-104160248	214	NFKB2_HUMAN	529-600	72	0	-	-
1.17b	ENST00000369966	17b	ENSE00000722732	chr10:104160412-104160581	170	NFKB2_HUMAN	600-656	57	0	-	-
1.18a	ENST00000369966	18a	ENSE00000722733	chr10:104160704-104160806	103	NFKB2_HUMAN	657-691	35	0	-	-
1.18c	ENST00000369966	18c	ENSE00000722734	chr10:104160937-104161088	152	NFKB2_HUMAN	691-741	51	0	-	-
1.19	ENST00000369966	19	ENSE00000722737	chr10:104161206-104161275	70	NFKB2_HUMAN	742-765	24	0	-	-
1.20	ENST00000369966	20	ENSE00000722739	chr10:104161502-104161674	173	NFKB2_HUMAN	765-822	58	0	-	-
1.21	ENST00000369966	21	ENSE00000722741	chr10:104161805-104161916	112	NFKB2_HUMAN	823-860	38	0	-	-
1.22b	ENST00000369966	22b	ENSE00001192799	chr10:104162009-104162281	273	NFKB2_HUMAN	860-900	41	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:296
 aligned with RELB_MOUSE | Q04863 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:296
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377      
           RELB_MOUSE    88 SCTLGRLVSPGPCPRPYLVITEQPKQRGMRFRYECEGRSAGSILGESSTEASKTLPAIELRDCGGLREVEVTACLVWKDWPHRVHPHSLVGKDCTDGVCRVRLRPHVSPRHSFNNLGIQCVRKKEIEAAIERKIQLGIDPYNAGSLKNHQEVDMNVVRICFQASYRDQQGHLHRMDPILSEPVYDKKSTNTSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTASWEGRADFSQADVHRQIAIVFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLPRDHDSY 383
               SCOP domains d3do7a1 A:88-278 automated matches                                                                                                                                                             d3do7a2 A:279-383 automated matches                                                                       SCOP domains
               CATH domains 3do7A01 A:88-274  [code=2.60.40.340, no name defined]                                                                                                                                      ----3do7A02 A:279-383 Immunoglobulins                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee......eee...........................eeeee...........eeee...........eeee......ee..........eee...eeee.....hhhhhhhhhhhh...................eeeeee.....................eee..........eeee...eee....eee.eee........eee............hhhhhhhhh...eee...........eeeeeeee..........eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------REL_2  PDB: A:100-277 UniProt: 100-277                                                                                                                                            ---------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------REL_1  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3do7 A  88 SCTLGRLVSPGPCPRPYLVITEQPKQRGMRFRYECEGRSAGSILGESSTEASKTQPAIELRDCGGLREVEVTACLVWKDWPHRVHPHSLVGKDCTDGVCRVRLRPHVSPRHSFNNLGIQCVRKKEIEAAIERKIQLGIDPYNAGSLKNHQEVDMNVVRICFQASYRDQQGHLHRMDPILSEPVYDKKSTNTSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTASWEGRADFSQADVHRQIAIVFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLPRDHDSY 383
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377

Chain B from PDB  Type:PROTEIN  Length:293
 aligned with NFKB2_HUMAN | Q00653 from UniProtKB/Swiss-Prot  Length:900

    Alignment length:293
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
          NFKB2_HUMAN    37 GPYLVIVEQPKQRGFRFRYGCEGPSHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSDPPRAHAHSLVGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKELKKVMDLSIVRLRFSAFLRASDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPLV 329
               SCOP domains d3do7b1 B:37-226 automated matches                                                                                                                                                            d3do7b2 B:227-329 automated matches                                                                     SCOP domains
               CATH domains 3do7B01 B:37-221  [code=2.60.40.340, no name defined]                                                                                                                                    ---3do7B02 B:225-322 Immunoglobulins                                                                 ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee............ee.hhh...................eeeee.....eeeeeeeee...........ee.........eeeee.....eee....eeee....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....eee....ee...ee.............ee...........eeeee............ee.............hhhhh....eeeee..............eee.............eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------REL_1  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4    Exon 1.5b  PDB: B:49-81          Exon 1.6  PDB: B:82-132 UniProt: 82-132            -----------------------------------Exon 1.8  PDB: B:168-221 UniProt: 168-221             ----------------------------------Exon 1.10  PDB: B:256-284    Exon 1.11  PDB: B:285-329 UniProt: 285-331    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.7  PDB: B:132-168             ----------------------------------------------------Exon 1.9  PDB: B:221-256            ------------------------------------------------------------------------- Transcript 1 (2)
                 3do7 B  37 GPYLVIVEQPKQRGFRFRYGCEGPSHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSDPPRAHAHSLVGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKELKKVMDLSIVRLRFSAFLRDSDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPLV 329
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326

Chain C from PDB  Type:DNA  Length:10
                                          
                 3do7 C   2 CGGGAATTCC  11
                                    11

Chain D from PDB  Type:DNA  Length:11
                                           
                 3do7 D  13 CGGGAATTCCC  23
                                    22

Chain E from PDB  Type:DNA  Length:11
                                           
                 3do7 E   2 CGGGAATTCCC  12
                                    11

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: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.340, no name defined] (30)

Mouse (Mus musculus) (2)

1a	3do7B01	B:37-221
1b	3do7A01	A:88-274

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

2a	3do7A02	A:279-383
2b	3do7B02	B:225-322

(no "Pfam Domain" information available for 3DO7)

Asymmetric Unit(hide GO term definitions)

Chain A (RELB_MOUSE | Q04863)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0001047	core promoter binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	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:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0038061	NIK/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
	GO:0045063	T-helper 1 cell differentiation	The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma.
	GO:0042088	T-helper 1 type immune response	An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0071470	cellular response to osmotic stress	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 stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
	GO:0032922	circadian regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
	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: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:0032688	negative regulation of interferon-beta production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta production.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0033256	I-kappaB/NF-kappaB complex	A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	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 (NFKB2_HUMAN | Q00653)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0038061	NIK/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0002268	follicular dendritic cell differentiation	The process in which a relatively unspecialized precursor cell acquires the specialized features of a follicular dendritic cell.
	GO:0002467	germinal center formation	The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation.
	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:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0032481	positive regulation of type I interferon production	Any process that activates or increases 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:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	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:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	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:0048536	spleen development	The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0033257	Bcl3/NF-kappaB2 complex	A protein complex containing one Bcl protein and one or more copies of NF-kappaB2; formation of complexes of different stoichiometry depends on the Bcl3:NF-kappaB2 ratio, and allow Bcl3 to exert different regulatory effects on NF-kappaB2-dependent transcription.
	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: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.

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	NFKB2_HUMAN \| Q00653	:	1a3q 2d96 4ot9
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(no "Related Entries Specified in the PDB File" available for 3DO7)

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