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- PDB-2mwx: The RING Domain of human Promyelocytic Leukemia Protein (PML) -

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Basic information

Entry
Database: PDB / ID: 2mwx
TitleThe RING Domain of human Promyelocytic Leukemia Protein (PML)
ComponentsProtein PML
KeywordsLIGASE / PML / RING finger / TRIM19 / E3 ligase
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 / oncogene-induced cell senescence / fibroblast migration / PML body organization / positive regulation of apoptotic process involved in mammary gland involution / SUMO binding / suppression of viral release by host ...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 / oncogene-induced cell senescence / fibroblast migration / PML body organization / positive regulation of apoptotic process involved in mammary gland involution / SUMO binding / suppression of viral release by host / negative regulation of mitotic cell cycle / endoplasmic reticulum calcium ion homeostasis / maintenance of protein location in nucleus / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / regulation of double-strand break repair / Regulation of RUNX1 Expression and Activity / positive regulation of extrinsic apoptotic signaling pathway / cobalt ion binding / negative regulation of interleukin-1 beta production / SUMOylation of ubiquitinylation proteins / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of telomere maintenance / protein sumoylation / regulation of cell adhesion / protein targeting / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / SUMOylation of DNA damage response and repair proteins / Dengue virus activates/modulates innate and adaptive immune responses / Regulation of TP53 Activity through Acetylation / positive regulation of defense response to virus by host / response to cytokine / negative regulation of angiogenesis / positive regulation of fibroblast proliferation / DNA damage response, signal transduction by p53 class mediator / Regulation of PTEN localization / intrinsic apoptotic signaling pathway in response to DNA damage / circadian regulation of gene expression / establishment of protein localization / negative regulation of cell growth / cellular senescence / PML body / regulation of circadian rhythm / Interferon gamma signaling / Transcriptional regulation of granulopoiesis / nuclear matrix / HCMV Early Events / nuclear membrane / protein-containing complex assembly / early endosome membrane / response to hypoxia / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / regulation of cell cycle / chromosome, telomeric region / transcription coactivator activity / protein stabilization / chromatin remodeling / negative regulation of cell population proliferation / protein heterodimerization activity / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / apoptotic process / nucleolus / regulation of DNA-templated transcription / endoplasmic reticulum membrane / protein homodimerization activity / DNA binding / DNA-templated transcription / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF3583 / : / PML-like, coiled-coil / PML, C-terminal domain / : / 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 ...Protein of unknown function DUF3583 / : / PML-like, coiled-coil / PML, C-terminal domain / : / 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 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHuang, S.Y. / Chang, C.F. / Fan, P.J. / Guntert, P. / Shih, H.M. / Huang, T.H.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: The RING domain of human promyelocytic leukemia protein (PML).
Authors: Huang, S.Y. / Chang, C.F. / Fang, P.J. / Naik, M.T. / Guntert, P. / Shih, H.M. / Huang, T.H.
History
DepositionDec 2, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein 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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein PML / Promyelocytic leukemia protein / RING finger protein 71 / Tripartite motif-containing protein 19


Mass: 6113.134 Da / Num. of mol.: 1 / Fragment: RING Domain, UNP residues 49-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML / Production host: Escherichia coli (E. coli) / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1923D 1H-13C NOESY aliphatic
11023D 1H-13C NOESY aromatic
11112D (HB)CB(CGCD)HD
11212D (HB)CB(CGCDCE)HE
11313D H(CCO)NH
11413D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] protein_1-1, 25 mM [U-98% 2H] TRIS-2, 100 mM sodium chloride-3, 0.2 mM TCEP-4, 1 mM zinc chloride-5, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] _protein1-6, 25 mM [U-98% 2H] TRIS-7, 100 mM sodium chloride-8, 0.2 mM TCEP-9, 1 mM zinc chloride-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein_1-1[U-99% 13C; U-99% 15N]1
25 mMTRIS-2[U-98% 2H]1
100 mMsodium chloride-31
0.2 mMTCEP-41
1 mMzinc chloride-51
1 mMprotein_1-6[U-99% 13C; U-99% 15N]2
25 mMTRIS-7[U-98% 2H]2
100 mMsodium chloride-82
0.2 mMTCEP-92
1 mMzinc chloride-102
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Uniform NMR SystemBrukerUniform NMR System6001
Bruker Uniform NMR SystemBrukerUniform NMR System8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.114Goddardchemical shift assignment
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
TALOS1.2009.0721.18Cornilescu, Delaglio and Baxtorsion angles prediction
CYANA3.9Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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