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- PDB-1bor: TRANSCRIPTION FACTOR PML, A PROTO-ONCOPROTEIN, NMR, 1 REPRESENTAT... -

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Entry
Database: PDB / ID: 1bor
TitleTRANSCRIPTION FACTOR PML, A PROTO-ONCOPROTEIN, NMR, 1 REPRESENTATIVE STRUCTURE AT PH 7.5, 30 C, IN THE PRESENCE OF ZINC
ComponentsTRANSCRIPTION FACTOR PML
KeywordsTRANSCRIPTION REGULATION / PROTO-ONCOGENE / NUCLEAR BODIES (PODS) / LEUKEMIA
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / PML body organization / SUMO binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / PML body organization / SUMO binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction / myeloid cell differentiation / maintenance of protein location in nucleus / protein-containing complex localization / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / oncogene-induced cell senescence / branching involved in mammary gland duct morphogenesis / Regulation of RUNX1 Expression and Activity / positive regulation of extrinsic apoptotic signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / cobalt ion binding / negative regulation of interleukin-1 beta production / intrinsic apoptotic signaling pathway in response to oxidative stress / SUMOylation of ubiquitinylation proteins / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / protein sumoylation / positive regulation of signal transduction by p53 class mediator / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of ubiquitin-dependent protein catabolic process / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein targeting / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / response to UV / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / positive regulation of defense response to virus by host / response to cytokine / transforming growth factor beta receptor signaling pathway / cellular response to interleukin-4 / Regulation of PTEN localization / DNA damage response, signal transduction by p53 class mediator / cellular response to leukemia inhibitory factor / negative regulation of angiogenesis / response to gamma radiation / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PML body / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / protein import into nucleus / Interferon gamma signaling / cellular senescence / protein-containing complex assembly / early endosome membrane / molecular adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / chromosome, telomeric region / response to hypoxia / regulation of cell cycle / protein stabilization / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / : / ANCHR-like B-box zinc-binding domain / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) ...Protein of unknown function DUF3583 / PML-like, coiled-coil / : / ANCHR-like B-box zinc-binding domain / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsBorden, K.L.B. / Freemont, P.S.
Citation
Journal: EMBO J. / Year: 1995
Title: The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML.
Authors: Borden, K.L. / Boddy, M.N. / Lally, J. / O'Reilly, N.J. / Martin, S. / Howe, K. / Solomon, E. / Freemont, P.S.
#1: Journal: Ann.N.Y.Acad.Sci. / Year: 1993
Title: The Ring Finger. A Novel Protein Sequence Motif Related to the Zinc Finger
Authors: Freemont, P.S.
History
DepositionSep 27, 1995Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2443
Polymers6,1131
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -REPRESENTATIVE STRUCTURE
Representative

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Components

#1: Protein TRANSCRIPTION FACTOR PML


Mass: 6113.134 Da / Num. of mol.: 1 / Fragment: RING FINGER DOMAIN, RESIDUES 49 - 104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P29590
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR ensembleConformer selection criteria: REPRESENTATIVE STRUCTURE / Conformers submitted total number: 1

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