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

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Basic information

Entry
Database: PDB / ID: 3vek
TitleBoth Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P1 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
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: 2.63 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 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
D: DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3')
E: DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3')
F: Erythroid transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,46320
Polymers51,5476
Non-polymers91614
Water00
1
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)26,1669
Polymers25,7743
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-157 kcal/mol
Surface area11970 Å2
MethodPISA
2
D: DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3')
E: DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3')
F: Erythroid transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,29711
Polymers25,7743
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-160 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.195, 62.415, 66.046
Angle α, β, γ (deg.)72.390, 74.570, 73.630
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21F
12C
22F
13A
23D
14B
24E

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSERCC201 - 3102 - 111
21ALAALASERSERFF201 - 3102 - 111
12ZNZNZNZNCJ - K401 - 402
22ZNZNZNZNFP - Q401 - 402
13DTDTDCDCAA1 - 201 - 20
23DTDTDCDCDD1 - 201 - 20
14DADADCDCBB21 - 401 - 20
24DADADCDCEE21 - 401 - 20

NCS ensembles :
ID
1
2
3
4

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Components

#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.: 2 / 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.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) synthetic construct (others)
#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.: 2 / 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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn

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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: 2.52 Å3/Da / Density % sol: 51.25 % / Mosaicity: 1.374 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 6000, 0.01M ZnCl2, 0.1M MES, pH 6.0, 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 15, 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: 2.63→50 Å / Num. all: 14526 / Num. obs: 14526 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.088 / Χ2: 1.081 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.63-2.684.40.3737180.963194.3
2.68-2.724.60.4087411.087196.1
2.72-2.784.70.5246841.08194.9
2.78-2.834.70.4657131.07196.2
2.83-2.894.60.3987150.994196.1
2.89-2.964.70.3947481.074195.8
2.96-3.044.80.3376841.032196.3
3.04-3.124.80.2577481.066196.6
3.12-3.214.70.1277151.017196.4
3.21-3.314.80.0887381.008196.9
3.31-3.434.80.1227191.033197.6
3.43-3.574.80.1247221.011197.4
3.57-3.734.80.1127130.995197.1
3.73-3.934.80.097650.96197.8
3.93-4.174.80.087300.98197.9
4.17-4.54.80.0737221.027198.2
4.5-4.954.80.0697471.161198.5
4.95-5.664.80.0587221.276198.5
5.66-7.134.80.0517521.49199.1
7.13-504.70.0367301.277198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.63 Å48.68 Å
Translation2.63 Å48.68 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 3VD6

3vd6


Resolution: 2.63→48.68 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.868 / WRfactor Rfree: 0.2823 / WRfactor Rwork: 0.2462 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7057 / SU B: 37.38 / SU ML: 0.349 / SU R Cruickshank DPI: 1.0666 / SU Rfree: 0.3568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.067 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 732 5.1 %RANDOM
Rwork0.2349 ---
obs0.2369 14469 96.32 %-
all-14469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 138.11 Å2 / Biso mean: 65.7281 Å2 / Biso min: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-1.22 Å20.59 Å2
2--4.33 Å21.29 Å2
3----4.85 Å2
Refinement stepCycle: LAST / Resolution: 2.63→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 1628 14 0 3154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0213362
X-RAY DIFFRACTIONr_bond_other_d0.0010.021808
X-RAY DIFFRACTIONr_angle_refined_deg0.9212.5434884
X-RAY DIFFRACTIONr_angle_other_deg0.88134440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7465188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.74621.84276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.96315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.4811522
X-RAY DIFFRACTIONr_chiral_restr0.040.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_mcbond_it0.512950
X-RAY DIFFRACTIONr_mcbond_other0.0812388
X-RAY DIFFRACTIONr_mcangle_it0.97731524
X-RAY DIFFRACTIONr_scbond_it1.2542412
X-RAY DIFFRACTIONr_scangle_it1.98863360
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C554MEDIUM POSITIONAL0.050.5
1C554MEDIUM THERMAL0.082
2C746MEDIUM POSITIONAL0.10.5
2C746MEDIUM THERMAL0.122
3A586MEDIUM POSITIONAL0.080.5
3A586MEDIUM THERMAL0.132
4B590MEDIUM POSITIONAL0.050.5
4B590MEDIUM THERMAL0.192
LS refinement shellResolution: 2.628→2.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 56 -
Rwork0.404 963 -
all-1019 -
obs--91.23 %
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)
12.30780.0522.17281.57691.195910.29460.259-0.2877-0.10890.08770.287-0.2276-0.14220.4533-0.54590.2476-0.0874-0.05920.2898-0.04050.2918-8.2088-9.199919.8625
26.04381.77083.81137.0782-1.60737.12150.2085-0.3944-0.49980.00870.0856-0.16610.07930.1913-0.29410.11520.0316-0.02160.40160.09180.1908-14.76-7.816.572
32.6098-0.0287-1.94791.54991.393211.20.2960.19710.0451-0.14180.2827-0.20010.00820.4031-0.57870.2350.09840.03220.2998-0.03490.2558-8.168124.148338.4492
410.7139-3.2362-2.18385.7082-0.11118.68640.23080.28990.4756-0.1873-0.0729-0.1623-0.13060.0823-0.15790.1111-0.0439-0.02550.31610.12470.1562-14.77422.74541.735
54.60960.3921.42152.5323-2.636610.6213-0.27850.2680.564-0.15560.1668-0.0154-0.9207-0.23240.11170.2309-0.01310.03550.02910.03180.2818-17.208-5.78719.335
63.2972-0.742-0.74323.3813-2.79239.752-0.2508-0.102-0.44870.26130.15090.08830.8548-0.12650.09990.20860.0091-0.0460.14550.06210.2487-17.18920.69139.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION1B21 - 40
3X-RAY DIFFRACTION2C201 - 310
4X-RAY DIFFRACTION3D1 - 20
5X-RAY DIFFRACTION3E21 - 40
6X-RAY DIFFRACTION4F201 - 310
7X-RAY DIFFRACTION5C401 - 402
8X-RAY DIFFRACTION6F401 - 402

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