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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 / 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 / protein-containing complex localization / maintenance of protein location in nucleus / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / branching involved in mammary gland duct morphogenesis / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / negative regulation of mitotic cell cycle / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / positive regulation of extrinsic apoptotic signaling pathway / cobalt ion binding / intrinsic apoptotic signaling pathway in response to oxidative stress / 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 / positive regulation of telomere maintenance / protein sumoylation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of signal transduction by p53 class mediator / 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 / response to UV / retinoic acid receptor signaling pathway / Regulation of PTEN localization / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / response to cytokine / cellular response to interleukin-4 / transforming growth factor beta receptor signaling pathway / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / DNA damage response, signal transduction by p53 class mediator / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PML body / nuclear matrix / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / HCMV Early Events / Interferon gamma signaling / intrinsic apoptotic signaling pathway in response to DNA damage / protein import into nucleus / cellular senescence / protein-containing complex assembly / early endosome membrane / nuclear membrane / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / response to hypoxia / chromosome, telomeric region / 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 / ubiquitin protein ligase binding / apoptotic process / 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 / 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) ...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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