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- PDB-2ma7: Solution NMR Structure of Zinc finger protein Eos from Homo sapie... -

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Basic information

Entry
Database: PDB / ID: 2ma7
TitleSolution NMR Structure of Zinc finger protein Eos from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7992A
ComponentsZinc finger protein Eos
KeywordsDNA BINDING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


bHLH transcription factor binding / protein homooligomerization / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding ...bHLH transcription factor binding / protein homooligomerization / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein Eos
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, null
Model detailslowest energy, model1
AuthorsPulavarti, S.V. / Mills, J.L. / Wang, D. / Jigabm, E. / Hamilton, K. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Zinc finger protein Eos from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7992A
Authors: Pulavarti, S.V. / Mills, J.L. / Wang, D. / Jigabm, E. / Hamilton, K. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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
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 finger protein Eos
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3402
Polymers8,2751
Non-polymers651
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 Zinc finger protein Eos / Ikaros family zinc finger protein 4


Mass: 8274.718 Da / Num. of mol.: 1 / Fragment: UNP residues 155-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKZF4, KIAA1782, ZNFN1A4 / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9H2S9
#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
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-13C HSQC aromatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D 1H-13C(CT) Aliphatic (28 ms)
1912D 1H-13C(CT) Aliphatic
11013D HBHA(CO)NH
1111gft43d (H)CCH COSY aliphatic
1121gft43d (H)CCH COSY aromatic
11313D (H)CCH-TOCSY
11412D 1H-15N HSQC (His longrange)
11512D 1H-13C(CT)HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] HR7992A.010, 5 mM DTT, 100 mM NaCl, 10 mM Tris-HCl pH 7.5, 0.02 % NaN3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [5% 13C; U-100% 15N] HR7992A.011, 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.02 mM NaN3, 5 mM DTT, 4 mM ZINC ION, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHR7992A.010-1[U-100% 13C; U-100% 15N]1
5 mMDTT-21
100 mMNaCl-31
10 mMTris-HCl pH 7.5-41
0.02 %NaN3-51
1 mMHR7992A.011-6[5% 13C; U-100% 15N]2
10 mMTris-HCl pH 7.5-72
100 mMNaCl-82
0.02 mMNaN3-92
5 mMDTT-102
4 mMZINC ION-112
Sample conditionspH: 75 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PROSAGuntertprocessing
PSVSBhattacharya, Montelionestructure validation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, null / Software ordinal: 1 / Details: energy minimization, null
NMR constraintsNOE constraints total: 369 / NOE intraresidue total count: 94 / NOE long range total count: 38 / NOE medium range total count: 102 / NOE sequential total count: 135 / Protein phi angle constraints total count: 23 / Protein psi angle constraints total count: 23
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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