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(-) Description

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

(-) Compounds

Molecule 1 - B-CELL LYMPHOMA 6 PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)+MAGIC
    Expression System Taxid469008
    Expression System VectorPET 14-15C
    FragmentC2H2-TYPE ZINC FINGERS 2 AND 3
    GeneBCL6, BCL5, LAZ3, ZBTB27, ZNF51
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBCL-6, B-CELL LYMPHOMA 5 PROTEIN, BCL-5, PROTEIN LAZ-3, ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27, ZINC FINGER PROTEIN 51

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:20 , CYS A:23 , HIS A:36 , HIS A:40BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARECYS A:48 , CYS A:51 , HIS A:64 , HIS A:68BINDING SITE FOR RESIDUE ZN A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.BCL6_HUMAN520-541
548-568
576-596
604-624
632-652
660-681
  2-
A:20-40
A:48-68
-
-
-
NMR Structure * (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.BCL6_HUMAN520-541
548-568
576-596
604-624
632-652
660-681
  2-
A:20-40
A:48-68
-
-
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3cENST000002320143cENSE00001512051chr3:187454357-187453878480BCL6_HUMAN-00--
1.4bENST000002320144bENSE00001377234chr3:187452695-18745265739BCL6_HUMAN-00--
1.5ENST000002320145ENSE00002178368chr3:187451491-187451321171BCL6_HUMAN1-54540--
1.6cENST000002320146cENSE00000781579chr3:187449718-187449497222BCL6_HUMAN54-128750--
1.7ENST000002320147ENSE00001609887chr3:187447809-187446838972BCL6_HUMAN128-4523250--
1.8ENST000002320148ENSE00001591359chr3:187446332-187446148185BCL6_HUMAN452-514630--
1.9ENST000002320149ENSE00001601736chr3:187444686-187444519168BCL6_HUMAN514-570571A:11-4232
1.10aENST0000023201410aENSE00001721923chr3:187443417-187443287131BCL6_HUMAN570-613441A:42-7433
1.11aENST0000023201411aENSE00001660239chr3:187442866-187442729138BCL6_HUMAN614-659460--
1.12bENST0000023201412bENSE00001928038chr3:187440389-187440186204BCL6_HUMAN660-706470--

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: C2H2-zf (71)

(-) Gene Ontology  (59, 59)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BCL6_HUMAN | P411821r28 1r29 1r2b 2en2 2eos 2yrm 3bim 3e4u 3lbz 4cp3 4u2m 5h7g 5h7h 5n1x 5n1z 5n20 5n21 5x4m 5x4n 5x4o 5x4p 5x4q

(-) Related Entries Specified in the PDB File

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