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- PDB-7n5t: ZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Prom... -

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Basic information

Entry
Database: PDB / ID: 7n5t
TitleZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Promoter (Oligo 5)
Components
  • DNA Strand I
  • DNA Strand II
  • Zinc finger and BTB domain-containing protein 7A
KeywordsDNA BINDING PROTEIN/DNA / Z=zinc-finger domain / gene expression / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of transcription regulatory region DNA binding / DNA-dependent protein kinase complex / negative regulation of androgen receptor signaling pathway / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / nuclear androgen receptor binding / erythrocyte maturation / regulation of alternative mRNA splicing, via spliceosome / histone acetyltransferase binding ...regulation of transcription regulatory region DNA binding / DNA-dependent protein kinase complex / negative regulation of androgen receptor signaling pathway / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / nuclear androgen receptor binding / erythrocyte maturation / regulation of alternative mRNA splicing, via spliceosome / histone acetyltransferase binding / SMAD binding / fat cell differentiation / negative regulation of Notch signaling pathway / protein localization to nucleus / B cell differentiation / transcription corepressor binding / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / site of double-strand break / chromatin organization / regulation of apoptotic process / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHorton, J.R. / Ren, R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Cell Rep / Year: 2021
Title: Structural basis for human ZBTB7A action at the fetal globin promoter.
Authors: Yang, Y. / Ren, R. / Ly, L.C. / Horton, J.R. / Li, F. / Quinlan, K.G.R. / Crossley, M. / Shi, Y. / Cheng, X.
History
DepositionJun 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 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: Zinc finger and BTB domain-containing protein 7A
X: DNA Strand I
Y: DNA Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0827
Polymers25,8203
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-32 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.479, 36.366, 176.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

#1: Protein Zinc finger and BTB domain-containing protein 7A / Factor binding IST protein 1 / FBI-1 / Factor that binds to inducer of short transcripts protein 1 ...Factor binding IST protein 1 / FBI-1 / Factor that binds to inducer of short transcripts protein 1 / HIV-1 1st-binding protein 1 / Leukemia/lymphoma-related factor / POZ and Krueppel erythroid myeloid ontogenic factor / POK erythroid myeloid ontogenic factor / Pokemon / Pokemon 1 / TTF-I-interacting peptide 21 / TIP21 / Zinc finger protein 857A


Mass: 16638.525 Da / Num. of mol.: 1 / Fragment: zinc finger domain (UNP residues 369-500)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB7A, FBI1, LRF, ZBTB7, ZNF857A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: O95365
#2: DNA chain DNA Strand I


Mass: 4731.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand II


Mass: 4450.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium bromide, 0.1 M Tris, pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→36.37 Å / Num. obs: 5536 / % possible obs: 99.3 % / Redundancy: 41.3 % / Biso Wilson estimate: 96.23 Å2 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.033 / Net I/σ(I): 24.7
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 17.4 % / Rmerge(I) obs: 4.27 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 542 / CC1/2: 0.873 / Rpim(I) all: 0.736 / % possible all: 97

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7N5U

7n5u


Resolution: 2.9→36.37 Å / SU ML: 0.4774 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.1388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3093 269 4.96 %
Rwork0.2467 5149 -
obs0.2498 5418 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.97 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 592 4 0 1433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331521
X-RAY DIFFRACTIONf_angle_d0.49812174
X-RAY DIFFRACTIONf_chiral_restr0.0339233
X-RAY DIFFRACTIONf_plane_restr0.0041183
X-RAY DIFFRACTIONf_dihedral_angle_d23.0582593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.47041280.34182466X-RAY DIFFRACTION95.72
3.65-36.370.27871410.22452683X-RAY DIFFRACTION99.05
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)
10.165710658836-2.61005421251-1.759729227052.5504526081-2.457360737516.80262042608-0.3817477033050.8593501275780.452012707710.6786432204930.07284221923480.2570211658730.145749791991-0.7753089089860.2060572873220.7012518627120.1837482645140.1180981466730.6946521366680.08871504256720.7674073305051.778028832070.14601732942938.2030526907
22.89686552643-3.04760042441.368182658337.677760967810.8608935940753.221928954110.520334250673-0.5418465996640.48707643247-2.099762468171.48140153588-0.171265469816-3.45582893535-0.346139155183-1.326185204681.597942194970.2166990292350.2972811051430.8485955074850.1451468628010.9994341301542.7513278271615.108246463831.8929580145
36.104216175340.836424969358-1.530360921760.470177236563-0.1356587167927.81287808482-0.9265025390840.8775518532650.511994923616-1.2864151820.990629251062-0.684906244727-1.79565787126-0.8838559729860.01998963487171.467436978-0.074282262750.3535220489970.5753181668580.01294935565740.98553089367212.311137469516.258175843817.798588482
45.059971296832.474206364340.5320041358454.220982907211.070675650526.76959409025-0.1152836273881.108102827520.528604652806-0.7111609974511.51187900618-0.3898134291540.8849478489520.184364988819-1.398457873060.8763299924430.24819540551-0.004684230486821.31344662107-0.02613331237670.84936176371112.5052597228-0.5903074857765.95479949531
54.95615077176-4.17040537926-1.811684492763.851316640172.812019443934.31682089504-0.3976982522030.0368204446272-1.99568799822-0.552747105859-1.001333134461.756037850882.66714463141-2.517257896060.7777710398941.51033103657-0.286191952299-0.01037624039721.14414720740.2348902350581.514435932756.00146353887-7.403852683729.25981310954
63.84205047308-0.57810458016-1.945099838612.36534947568-0.2937001772236.11314648411-0.1616299201590.197829279161-0.301537280663-0.6088848886810.243388353586-0.239152133752-0.5169153949940.0408334617254-0.1712914304510.7548562183230.1301761025380.0500716303160.8713037402410.004721153024970.887927326845.879133359332.7122256220622.0449688987
71.30306031618-0.872040650852-0.02289211900535.0460969317-1.720542289465.045587076710.137258595611-0.218376663941-0.841979200377-0.5003262372750.56829189752-0.6006791398590.720035203134-1.06999357492-0.4344987267110.62055283484-0.2711891208730.1290469699881.337611551430.01592525649361.023703555426.788204115983.2473814633527.274222201
82.76629482112-3.076838437730.405256242227.752384074042.007789905571.67687847090.736955942538-0.5238441205062.468179909490.1579799677830.823386668174-0.561495155021-0.2516742357490.838019533171-0.6983955124971.227818602980.2087662051770.001771273555072.379230394580.2847141986062.03216106132-7.372715712848.627954618687.06921336237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 381 through 421 )AA381 - 4211 - 41
22chain 'A' and (resid 422 through 433 )AA422 - 43342 - 53
33chain 'A' and (resid 434 through 460 )AA434 - 46054 - 80
44chain 'A' and (resid 461 through 477 )AA461 - 47781 - 97
55chain 'A' and (resid 478 through 491 )AA478 - 49198 - 111
66chain 'X' and (resid 2 through 15 )XF2 - 15
77chain 'Y' and (resid 1 through 13 )YG1 - 13
88chain 'Y' and (resid 14 through 15 )YG14 - 15

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