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- PDB-2ly9: Solution NMR Structure of Homeobox 2 Domain from Human ZHX1 repre... -

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Basic information

Entry
Database: PDB / ID: 2ly9
TitleSolution NMR Structure of Homeobox 2 Domain from Human ZHX1 repressor, Northeast Structural Genomics Consortium (NESG) Target HR7907F
ComponentsZinc fingers and homeoboxes protein 1
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm ...cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Homez, homeobox domain / ZHX, C2H2 finger domain / Homeodomain leucine-zipper encoding, Homez / Zinc-fingers and homeoboxes C2H2 finger domain / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / zinc finger / Homeodomain-like ...Homez, homeobox domain / ZHX, C2H2 finger domain / Homeodomain leucine-zipper encoding, Homez / Zinc-fingers and homeoboxes C2H2 finger domain / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / zinc finger / Homeodomain-like / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc fingers and homeoboxes protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsXu, X. / Eletsky, A. / Mills, J.L. / Pulavarti, S.V.S.R.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. ...Xu, X. / Eletsky, A. / Mills, J.L. / Pulavarti, S.V.S.R.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Homeobox 2 Domain from Human ZHX1 repressor, Northeast Structural Genomics Consortium (NESG) Target HR7907F
Authors: Xu, X. / Eletsky, A. / Mills, J.L. / Pulavarti, S.V.S.R.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionSep 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 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: Zinc fingers and homeoboxes protein 1


Theoretical massNumber of molelcules
Total (without water)8,7101
Polymers8,7101
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc fingers and homeoboxes protein 1


Mass: 8710.016 Da / Num. of mol.: 1 / Fragment: DNA binding Homeobox 2 residues 462-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZHX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9UKY1

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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 HNCO
141(4,3)D GFT CABCA(CO)NHN
151(4,3)D GFT HNNCABCA
1622D 1H-13C HSQC
171(4,3)D GFT (H)CCH-COSY alipahtic
1813D (H)CCH-TOCSY aliphatic
1913D 13C/15N-edited NOESY
1101(4,3)D GFT HABCAB(CO)NH
11113D (H)CCH-COSY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 13C; U-100% 15N] HR7907F, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [5% 13C; U-100% 15N] HR7907F, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMHR7907F-1[U-100% 13C; U-100% 15N]1
0.02 %sodium azide-21
10 mMDTT-31
5 mMcalcium chloride-41
100 mMsodium chloride-51
1 %Proteinase Inhibitors-61
20 mMMES-71
50 uMDSS-81
0.3 mMHR7907F-9[5% 13C; U-100% 15N]2
0.02 %sodium azide-102
10 mMDTT-112
5 mMcalcium chloride-122
100 mMsodium chloride-132
1 %Proteinase Inhibitors-142
20 mMMES-152
50 uMDSS-162
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AS-DP1Huang, Tejero, Powers and Montelionedata analysis
AS-DP1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD NMR ENSEMBLE INFORMATION
NMR constraintsNOE constraints total: 875 / NOE intraresidue total count: 278 / NOE long range total count: 176 / NOE medium range total count: 217 / NOE sequential total count: 204 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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