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- PDB-3vd6: Both Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Sit... -

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Basic information

Entry
Database: PDB / ID: 3vd6
TitleBoth Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P21 Crystal Form
Components
  • DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3')
  • DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3')
  • Erythroid transcription factor
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / ZINC FINGER / TRANSCRIPTION FACTOR / DNA BINDING / NUCLEUS / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / myeloid cell apoptotic process / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development ...regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / myeloid cell apoptotic process / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Sertoli cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / dendritic cell differentiation / cellular response to follicle-stimulating hormone stimulus / negative regulation of bone mineralization / Factors involved in megakaryocyte development and platelet production / negative regulation of myeloid cell apoptotic process / positive regulation of mast cell degranulation / myeloid cell differentiation / C2H2 zinc finger domain binding / embryonic hemopoiesis / platelet formation / bone mineralization / positive regulation of osteoblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell fate commitment / animal organ regeneration / cis-regulatory region sequence-specific DNA binding / erythrocyte development / cellular response to cAMP / homeostasis of number of cells within a tissue / transcription repressor complex / erythrocyte differentiation / positive regulation of erythrocyte differentiation / transcription coregulator binding / protein-DNA complex / chromatin DNA binding / transcription coactivator binding / platelet aggregation / positive regulation of peptidyl-tyrosine phosphorylation / p53 binding / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / chromatin binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Erythroid transcription factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsJacques, D.A. / Ripin, N. / Wilkinson-White, L.E. / Guss, J.M. / Matthews, J.M.
CitationJournal: Protein Sci. / Year: 2015
Title: GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA.
Authors: Wilkinson-White, L. / Lester, K.L. / Ripin, N. / Jacques, D.A. / Mitchell Guss, J. / Matthews, J.M.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3')
B: DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3')
C: Erythroid transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0297
Polymers25,7743
Non-polymers2554
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-35 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.331, 37.401, 65.484
Angle α, β, γ (deg.)90.000, 98.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3')


Mass: 6114.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3')


Mass: 6151.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules C

#3: Protein Erythroid transcription factor / Eryf1 / GATA-binding factor 1 / GATA-1 / GF-1 / NF-E1 DNA-binding protein


Mass: 13507.752 Da / Num. of mol.: 1 / Fragment: N and C Fingers, residues 200-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gata1 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P17679

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Non-polymers , 3 types, 97 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.82 % / Mosaicity: 1.89 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M BISTRIS, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 12, 2011
RadiationMonochromator: CONFOCAL MAXFLUX MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→15 Å / Num. all: 18281 / Num. obs: 18281 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.049 / Χ2: 1.048 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.013.40.588931.094199.9
2.01-2.053.40.5099101.084199.5
2.05-2.093.40.4779041.071198.5
2.09-2.133.40.418881.0741100
2.13-2.183.30.3559291.063199.8
2.18-2.233.40.3058801.09199.4
2.23-2.283.40.2679201.044199.9
2.28-2.353.40.2469231.072199.8
2.35-2.423.40.1748861.079199.8
2.42-2.493.40.1769341.0731100
2.49-2.583.50.1448951.0821100
2.58-2.683.50.1199380.9721100
2.68-2.813.60.0929171.099199.9
2.81-2.953.60.0799041.0721100
2.95-3.143.60.0629310.981199.7
3.14-3.383.60.0478721.082195.2
3.38-3.713.70.049280.967199.8
3.71-4.243.70.0379181.059199.1
4.24-5.33.60.0379361.029199.5
5.3-153.60.0359750.92199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å38.45 Å
Translation3.5 Å38.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DFX

3dfx


Resolution: 1.98→14.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2715 / WRfactor Rwork: 0.2401 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7744 / SU B: 11.089 / SU ML: 0.136 / SU R Cruickshank DPI: 0.1751 / SU Rfree: 0.1551 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 887 4.9 %RANDOM
Rwork0.2182 ---
obs0.2196 18203 98.83 %-
all-18203 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.56 Å2 / Biso mean: 55.616 Å2 / Biso min: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å2-3.22 Å2
2--0.27 Å20 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.98→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 814 7 93 1670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211690
X-RAY DIFFRACTIONr_bond_other_d0.0010.02907
X-RAY DIFFRACTIONr_angle_refined_deg1.082.542455
X-RAY DIFFRACTIONr_angle_other_deg0.93532229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.986596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67122.05139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09715132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3881511
X-RAY DIFFRACTIONr_chiral_restr0.0440.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_mcbond_it0.9172481
X-RAY DIFFRACTIONr_mcbond_other0.1792195
X-RAY DIFFRACTIONr_mcangle_it1.6553770
X-RAY DIFFRACTIONr_scbond_it2.02941209
X-RAY DIFFRACTIONr_scangle_it2.84461684
LS refinement shellResolution: 1.979→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 58 -
Rwork0.376 1200 -
all-1258 -
obs--95.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9846-1.13790.99642.9715-0.14383.0370.04060.0754-0.2549-0.1552-0.08620.12780.11460.16880.04550.12660.02270.04570.1049-0.02280.046316.7333-0.014316.3636
23.2619-1.26970.9025.031-0.85924.9215-0.0459-0.2644-0.00590.3362-0.0151-0.2997-0.19260.39260.0610.1546-0.0237-0.01480.1724-0.0220.040323.19234.529127.581
34.7485-0.81011.58394.03361.46456.981-0.16290.67630.481-0.6442-0.14710.1271-0.46170.34810.310.2220.0176-0.06530.1210.04450.118610.6548.56916.1156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION1B21 - 40
3X-RAY DIFFRACTION2C201 - 241
4X-RAY DIFFRACTION2C500
5X-RAY DIFFRACTION2C502
6X-RAY DIFFRACTION3C256 - 309
7X-RAY DIFFRACTION3C501

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