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- PDB-2l8e: Solution NMR structure of FCS domain of Human Polyhomeotic Homolo... -

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Basic information

Entry
Database: PDB / ID: 2l8e
TitleSolution NMR structure of FCS domain of Human Polyhomeotic Homolog 1 (HPH1)
ComponentsPolyhomeotic-like protein 1
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


: / PRC1 complex / multicellular organism development / PcG protein complex / negative regulation of G0 to G1 transition / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / SUMOylation of DNA damage response and repair proteins ...: / PRC1 complex / multicellular organism development / PcG protein complex / negative regulation of G0 to G1 transition / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / histone binding / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #160 / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #160 / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyhomeotic-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsIlangovan, U. / Kim, C.
CitationJournal: To be Published
Title: 1H, 15N and 13C assigned chemical shifts of FCS domain from human polyhomeotic homolog 1
Authors: Wang, R. / Ilangovan, U. / Kim, C.
History
DepositionJan 11, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyhomeotic-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5562
Polymers5,4901
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Polyhomeotic-like protein 1 / hPH1 / Early development regulatory protein 1


Mass: 5490.305 Da / Num. of mol.: 1 / Fragment: FCS-type zinc finger domain residues 783-828
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHC1, EDR1, PH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P78364
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1213D HNHA
1313D 1H-15N NOESY
1413D 1H-15N TOCSY
1522D 1H-13C HSQC
1623D CBCA(CO)NH
1723D HN(CA)CB
1823D C(CO)NH
1923D (H)CCH-TOCSY
1103ct-HSQC
1113hbcbcgcdhdgp
1123hbcbcgcdcehegp

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 15N] Zn bound FCS domain of hPh1, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM [U-95% 13C; U-95% 15N] Zn bound FCS domain of hPh1, 95% H2O/5% D2O95% H2O/5% D2O
31.5 mM [U-10% 13C; U-99% 15N] Zn bound FCS domain of hPh1, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMZn bound FCS domain of hPh1-1[U-100% 15N]1
1.5 mMZn bound FCS domain of hPh1-2[U-95% 13C; U-95% 15N]2
1.5 mMZn bound FCS domain of hPh1-3[U-10% 13C; U-99% 15N]3
Sample conditionsIonic strength: 0.050 / pH: 6.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
TopSpinBruker Biospincollection
ARIArefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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