2LCE - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   CHEMICAL SHIFT ASSIGNMENT OF HR4436B FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM

Authors :   H. Lee, R. Shastry, C. Ciccosanti, H. Janjua, T. B. Acton, R. Xiao, J. K. E G. T. Montelione, J. H. Prestegard, Northeast Structural Genomics Consortium (Nesg)

Date :   28 Apr 11 (Deposition) - 18 May 11 (Release) - 22 Feb 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (10x)
NMR Structure *: A  (1x)

Keywords :   Structural Genomics, Northeast Structural Genomics Consortium, Nesg, Psi-Biology, Protein Structure Initiative, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Lee, G. T. Montelione, J. H. Prestegard
Solution Structure Of Hr4436B.
To Be Published
PubMed: search

Molecule 1 - B-CELL LYMPHOMA 6 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	469008
	Expression System Vector	:	PET 14-15C
	Fragment	:	C2H2-TYPE ZINC FINGERS 2 AND 3
	Gene	:	BCL6, BCL5, LAZ3, ZBTB27, ZNF51
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BCL-6, B-CELL LYMPHOMA 5 PROTEIN, BCL-5, PROTEIN LAZ-3, ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27, ZINC FINGER PROTEIN 51

		1
NMR Structure (10x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

NMR Structure * (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:20 , CYS A:23 , HIS A:36 , HIS A:40	BINDING SITE FOR RESIDUE ZN A 200
2	AC2	SOFTWARE	CYS A:48 , CYS A:51 , HIS A:64 , HIS A:68	BINDING SITE FOR RESIDUE ZN A 300

(no "SS Bond" information available for 2LCE)

(no "Cis Peptide Bond" information available for 2LCE)

(no "SAP(SNP)/Variant" information available for 2LCE)

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	BCL6_HUMAN	520-541 548-568 576-596 604-624 632-652 660-681	2	- A:20-40 A:48-68 - - -

NMR Structure * (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	BCL6_HUMAN	520-541 548-568 576-596 604-624 632-652 660-681	2	- A:20-40 A:48-68 - - -

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3c	ENST00000232014	3c	ENSE00001512051	chr3:187454357-187453878	480	BCL6_HUMAN	-	0	0	-	-
1.4b	ENST00000232014	4b	ENSE00001377234	chr3:187452695-187452657	39	BCL6_HUMAN	-	0	0	-	-
1.5	ENST00000232014	5	ENSE00002178368	chr3:187451491-187451321	171	BCL6_HUMAN	1-54	54	0	-	-
1.6c	ENST00000232014	6c	ENSE00000781579	chr3:187449718-187449497	222	BCL6_HUMAN	54-128	75	0	-	-
1.7	ENST00000232014	7	ENSE00001609887	chr3:187447809-187446838	972	BCL6_HUMAN	128-452	325	0	-	-
1.8	ENST00000232014	8	ENSE00001591359	chr3:187446332-187446148	185	BCL6_HUMAN	452-514	63	0	-	-
1.9	ENST00000232014	9	ENSE00001601736	chr3:187444686-187444519	168	BCL6_HUMAN	514-570	57	1	A:11-42	32
1.10a	ENST00000232014	10a	ENSE00001721923	chr3:187443417-187443287	131	BCL6_HUMAN	570-613	44	1	A:42-74	33
1.11a	ENST00000232014	11a	ENSE00001660239	chr3:187442866-187442729	138	BCL6_HUMAN	614-659	46	0	-	-
1.12b	ENST00000232014	12b	ENSE00001928038	chr3:187440389-187440186	204	BCL6_HUMAN	660-706	47	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(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:64
 aligned with BCL6_HUMAN | P41182 from UniProtKB/Swiss-Prot  Length:706

    Alignment length:64
                                   548       558       568       578       588       598    
           BCL6_HUMAN   539 QTHSDKPYKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTHTRIHSGEKPY 602
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------zf-H2C2_2-2lceA Pfam domains (1)
           Pfam domains (2) -------------------------------------------------zf-H2C2_2-2lceA Pfam domains (2)
         Sec.struct. author ..................hhhhhhhhhhhhh....ee......ee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZIN------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   ------ PROSITE
           Transcript 1 (1) -------------------------------Exon 1.10a  PDB: A:42-74          Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:11-42          -------------------------------- Transcript 1 (2)
                 2lce A  11 MTHSDKPYKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTHTRIHSGEKPY  74
                                    20        30        40        50        60        70

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 2LCE)

(no "CATH Domain" information available for 2LCE)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C2H2-zf (71)

Family: zf-H2C2_2 (52)

Homo sapiens (Human) (37)

1a	zf-H2C2_2-2lceA01	A:60-74
1b	zf-H2C2_2-2lceA02	A:60-74

NMR Structure(hide GO term definitions)

Chain A (BCL6_HUMAN | P41182)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0031490	chromatin DNA binding	Interacting selectively and non-covalently with DNA that is assembled into chromatin.
	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:0001161	intronic transcription regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with an intronic DNA sequence that regulates the transcription of the transcript it is contained within.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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:0001227	transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0006974	cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0048821	erythrocyte development	The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
	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: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:0030099	myeloid cell differentiation	The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
	GO:0002903	negative regulation of B cell apoptotic process	Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell apoptotic process.
	GO:0045746	negative regulation of Notch signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
	GO:0035024	negative regulation of Rho protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
	GO:0045629	negative regulation of T-helper 2 cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0045596	negative regulation of cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0001953	negative regulation of cell-matrix adhesion	Any process that stops, prevents, or reduces the rate or extent of cell adhesion to the extracellular matrix.
	GO:2000773	negative regulation of cellular senescence	Any process that stops, prevents or reduces the frequency, rate or extent of cellular senescence.
	GO:0048294	negative regulation of isotype switching to IgE isotypes	Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching to IgE isotypes.
	GO:0032764	negative regulation of mast cell cytokine production	Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell cytokine 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:0002829	negative regulation of type 2 immune response	Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response.
	GO:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0051272	positive regulation of cellular component movement	Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
	GO:0031065	positive regulation of histone deacetylation	Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones.
	GO:0045666	positive regulation of neuron differentiation	Any process that activates or increases the frequency, rate or extent of neuron differentiation.
	GO:0000060	protein import into nucleus, translocation	A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0002634	regulation of germinal center formation	Any process that modulates the frequency, rate, or extent of germinal center formation.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	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:0043380	regulation of memory T cell differentiation	Any process that modulates the frequency, rate, or extent of memory T cell differentiation.
	GO:0050767	regulation of neurogenesis	Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
	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:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0042092	type 2 immune response	An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects.
cellular component
	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.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

NMR Structure
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	2lce
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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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