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- PDB-7n5w: ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (... -

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Basic information

Entry
Database: PDB / ID: 7n5w
TitleZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 23)
Components
  • DNA Strand I
  • DNA Strand II
  • Zinc finger and BTB domain-containing protein 7A
KeywordsDNA BINDING PROTEIN/DNA / 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 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 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 / : / 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: 2.24 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: J.Biol.Chem. / Year: 2023
Title: Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia.
Authors: Ren, R. / Horton, J.R. / Chen, Q. / Yang, J. / Liu, B. / Huang, Y. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionJun 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.title / _citation_author.name
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Feb 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 25, 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)25,66510
Polymers25,2203
Non-polymers4447
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-7 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.157, 103.429, 83.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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: 15424.003 Da / Num. of mol.: 1 / Fragment: zinc finger domain (UNP residues 380-500)
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

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DNA chain , 2 types, 2 molecules XY

#2: DNA chain DNA Strand I


Mass: 4916.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand II


Mass: 4880.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 42 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium malonate, pH 5.0, 12% 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: Apr 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→37.08 Å / Num. obs: 25580 / % possible obs: 89.5 % / Redundancy: 11.4 % / Biso Wilson estimate: 53.33 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.035 / Net I/σ(I): 18.3
Reflection shellResolution: 2.24→2.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1003 / CC1/2: 0.598 / Rpim(I) all: 0.47 / % possible all: 43.6

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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: 2.24→37.08 Å / SU ML: 0.3644 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 1284 5.05 %
Rwork0.1897 24155 -
obs0.1916 25439 85.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.88 Å2
Refinement stepCycle: LAST / Resolution: 2.24→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 650 19 35 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561426
X-RAY DIFFRACTIONf_angle_d0.77012047
X-RAY DIFFRACTIONf_chiral_restr0.0457222
X-RAY DIFFRACTIONf_plane_restr0.0068150
X-RAY DIFFRACTIONf_dihedral_angle_d26.2861576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.330.398590.35071053X-RAY DIFFRACTION33.64
2.33-2.440.322970.33291918X-RAY DIFFRACTION61.45
2.44-2.570.31121370.3152633X-RAY DIFFRACTION84.89
2.57-2.730.42481630.33983047X-RAY DIFFRACTION97.21
2.73-2.940.27721610.25443108X-RAY DIFFRACTION99.85
2.94-3.230.33871650.23223089X-RAY DIFFRACTION98.88
3.23-3.70.23331710.17653088X-RAY DIFFRACTION98.67
3.7-4.660.16711670.14943100X-RAY DIFFRACTION99.85
4.66-37.080.17131640.14343119X-RAY DIFFRACTION99.58
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)
18.97683142952-1.115304326832.426876034848.929904961494.136904124724.328013657390.953935824163-0.145151547187-1.059346137430.451277043034-0.4085859389280.4339842524382.82337932704-0.955540999181-0.5298556301860.80564493953-0.01743577727310.06151012949440.594598628048-0.05440965698760.655347894058-20.3775624028-35.8326842634-32.6468820486
24.244201587830.730305831359-3.653128522734.93564937902-4.56286807246.346713279610.7520187036262.59572598294-0.119685529205-0.965412980054-0.203066076606-0.0939380734420.965776006715-0.485606713261-0.483626221950.5460359606160.0559771534256-0.0924743961491.0749565106-0.00990452672240.500654684021-28.7328353115-27.7339416529-34.7443066164
32.94644847396-0.7688865052360.144615003790.780802303410.7349423002447.09420883092-0.0660882557687-0.130390762077-0.0533831301510.08358719950020.03416643883770.0736726172751-0.0272829631738-0.9561078108870.04620407793610.278873218592-0.0222436654985-0.01553974594130.4477982534680.04449729366480.349766324735-29.1439426123-24.6158731567-18.4837660168
48.022936247274.516581757032.509560755368.014997575034.949571299533.179850946120.00608974556481-0.2122588789070.378684582325-0.134837342547-0.0884414083905-0.81536135632-0.01405477466071.319535726180.06863219912520.4393773301280.0426539886292-0.05820520706310.5216536960210.01044099207770.386011565304-22.834133534-20.3249111751-9.1613932621
55.37198742854-1.847157030710.1590062857253.01887165188-4.736739173399.42945014570.8146887828510.249926421843-0.144995818339-0.435930652549-1.007881066530.624689570949-0.8436551476321.330023191110.2392857496290.5573595042790.0335577349595-0.08063399854950.577235319232-0.09478912534110.467311994559-23.9661510252-16.93283050661.56643395904
68.781592691430.006821451766070.9532446885917.57031481394-1.436288679297.556268554790.2520001243430.529434703634-0.770246510962-0.40482129656-0.1758555257310.6160183241431.13298427907-1.47712108283-0.06540375017840.502326798863-0.159926289055-0.1021696554380.69024092901-0.02737172647480.570150245661-28.666087684-27.9832709564.07536547541
72.95246340491-0.5423440608412.003965392162.0741223114-2.224008749464.670881054450.1019738510.07071633637940.5417201618671.51715372359-1.16846396975-1.15618025995-1.030154330280.5056511063640.8882353329741.13906280714-0.13254498691-0.05209415235440.527466231226-0.0311726273421.25322558229-18.037252684-1.57220984166-21.6801955431
83.603630626141.65126407231-0.7099878673794.10263342754-2.723954801914.74285380834-0.3104322332160.0569988605497-0.2175699520160.434608860522-0.134802180192-0.600249532353-0.07094163324491.007289540390.3449545348270.3896996942060.03636921041380.02577843754120.497010567103-0.01593935606690.441751058215-15.5500653611-27.0332675851-22.9015031344
96.337807317023.27710741154-2.081775240472.54948995263-0.186510876382.061203166010.403880801329-0.956090997647-0.6018803991290.553464735819-0.37738177220.43851702670.9047156753360.3476500910190.02706745797350.5367237296020.0285545887899-0.0281255139490.5266302188020.06024910397520.720756686511-18.9865586194-31.4756634687-14.7546897379
102.554814361492.78255962220.8960991869294.02033879272.487623518053.941777592780.08397974063230.252016586991.08966405359-0.0494807571038-0.7774402584130.810227931204-1.58978403303-0.1456001875260.6747097444630.962007739057-0.062224821228-0.06800195764590.517805853825-0.01318795593340.904774897545-17.984905114-6.28688275337-21.5075828839
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 377 through 383 )AA377 - 3831 - 7
22chain 'A' and (resid 384 through 389 )AA384 - 3898 - 13
33chain 'A' and (resid 390 through 421 )AA390 - 42114 - 45
44chain 'A' and (resid 422 through 431 )AA422 - 43146 - 55
55chain 'A' and (resid 432 through 436 )AA432 - 43656 - 60
66chain 'A' and (resid 437 through 461 )AA437 - 46161 - 85
77chain 'X' and (resid -1 through 8 )XF-1 - 8
88chain 'X' and (resid 9 through 14 )XF9 - 14
99chain 'Y' and (resid 1 through 5 )YJ1 - 5
1010chain 'Y' and (resid 6 through 16 )YJ6 - 16

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