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- PDB-2mvw: Solution structure of the TRIM19 B-box1 (B1) of human promyelocyt... -

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Basic information

Entry
Database: PDB / ID: 2mvw
TitleSolution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)
ComponentsProtein PML
KeywordsMETAL BINDING PROTEIN / PML / B box / TRIM19 / E3 ligase
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / suppression of viral release by host / PML body organization / SUMO binding / fibroblast migration ...regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / suppression of viral release by host / PML body organization / SUMO binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / : / regulation of double-strand break repair / myeloid cell differentiation / positive regulation of telomere maintenance / SMAD protein signal transduction / maintenance of protein location in nucleus / protein-containing complex localization / endoplasmic reticulum calcium ion homeostasis / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of extrinsic apoptotic signaling pathway / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / SUMO transferase activity / branching involved in mammary gland duct morphogenesis / negative regulation of interleukin-1 beta production / intrinsic apoptotic signaling pathway in response to oxidative stress / SUMOylation of ubiquitinylation proteins / cobalt ion binding / SMAD binding / entrainment of circadian clock by photoperiod / protein monoubiquitination / positive regulation of signal transduction by p53 class mediator / negative regulation of telomere maintenance via telomerase / protein sumoylation / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / cell fate commitment / protein targeting / cellular response to interleukin-4 / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / Regulation of TP53 Activity through Acetylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / response to cytokine / cellular response to leukemia inhibitory factor / response to gamma radiation / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PML body / nuclear matrix / HCMV Early Events / Transcriptional regulation of granulopoiesis / protein import into nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon gamma signaling / ubiquitin protein ligase activity / cellular senescence / positive regulation of fibroblast proliferation / early endosome membrane / protein-containing complex assembly / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / molecular adaptor activity / transcription coactivator activity / protein stabilization / response to hypoxia / regulation of cell cycle / 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 / regulation of DNA-templated transcription / endoplasmic reticulum membrane / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / : / B-box zinc finger / 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 ...Protein of unknown function DUF3583 / PML-like, coiled-coil / : / B-box zinc finger / 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 / DGSA-distance geometry simulated annealing
AuthorsHuang, S. / Naik, M.T. / Fan, P. / Wang, Y. / Chang, C. / Huang, T.
CitationJournal: J.Biomol.Nmr / Year: 2014
Title: The B-box 1 dimer of human promyelocytic leukemia protein.
Authors: Huang, S.Y. / Naik, M.T. / Chang, C.F. / Fang, P.J. / Wang, Y.H. / Shih, H.M. / Huang, T.H.
History
DepositionOct 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
B: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1456
Polymers11,8842
Non-polymers2624
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: 5941.795 Da / Num. of mol.: 2 / Fragment: UNP residues 120-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29590
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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(CCO)NH
1713D C(CO)NH
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11012D 1H-1H COSY
11112D 1H-1H NOESY
11213D 1H-13C NOESY aliphatic
11323D 1H-13C NOESY aliphatic
114313C-edited/12C-filtered 3D NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] PML B1 box, 25 mM [U-98% 2H] TRIS, 100 mM sodium chloride, 0.2 mM TCEP, 1 mM zinc chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] PML B1 box, 25 mM [U-98% 2H] TRIS, 100 mM sodium chloride, 0.2 mM TCEP, 1 mM zinc chloride, 100% D2O100% D2O
30.5 mM [U-99% 13C; U-99% 15N] PML B1 box, 0.5 mM PML B1 box, 25 mM [U-98% 2H] TRIS, 100 mM sodium chloride, 0.2 mM TCEP, 1 mM zinc chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPML B1 box-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 mMPML B1 box-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
0.5 mMPML B1 box-11[U-99% 13C; U-99% 15N]3
0.5 mMPML B1 box-123
25 mMTRIS-13[U-98% 2H]3
100 mMsodium chloride-143
0.2 mMTCEP-153
1 mMzinc chloride-163
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerField strength (MHz)Spectrometer-ID
Bruker Uniform NMR SystemBruker6001
Bruker Uniform NMR SystemBruker8002
Bruker Uniform NMR SystemBruker8503

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.9Guntert, Mumenthaler and Wuthrichgeometry optimization
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
Sparky3.114Goddardchemical shift assignment
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
TALOS1.2009.0721.18Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1391 / NOE long range total count: 393 / NOE medium range total count: 213 / Protein phi angle constraints total count: 42 / Protein psi angle constraints total count: 42
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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