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- PDB-8h9h: Crystal structure of ZBTB7A in complex with GACCC-containing sequence -

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Basic information

Entry
Database: PDB / ID: 8h9h
TitleCrystal structure of ZBTB7A in complex with GACCC-containing sequence
Components
  • DNA (5'-D(*TP*AP*AP*GP*GP*AP*CP*CP*CP*AP*GP*AP*T)-3')
  • DNA (5'-D(P*AP*AP*TP*CP*TP*GP*GP*GP*TP*CP*CP*TP*T)-3')
  • Zinc finger and BTB domain-containing protein 7A
KeywordsDNA BINDING PROTEIN / ZBTB7A / primed to naive transition / transcription regulation
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: ZBTB7A regulates primed-to-naive transition of pluripotent stem cells via recognition of the PNT-associated sequence by zinc fingers 1-2 and recognition of gamma-globin -200 gene element by zinc fingers 1-4.
Authors: Yang, Y. / Xiao, L. / Xue, Y. / Idris, M.O. / Liu, J. / Pei, D. / Shi, Y. / Liao, B. / Li, F.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Refinement description / Category: 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*AP*AP*GP*GP*AP*CP*CP*CP*AP*GP*AP*T)-3')
B: DNA (5'-D(P*AP*AP*TP*CP*TP*GP*GP*GP*TP*CP*CP*TP*T)-3')
G: Zinc finger and BTB domain-containing protein 7A
F: Zinc finger and BTB domain-containing protein 7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4468
Polymers28,1844
Non-polymers2624
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-26 kcal/mol
Surface area10740 Å2
Unit cell
Length a, b, c (Å)63.542, 63.542, 201.586
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: DNA chain DNA (5'-D(*TP*AP*AP*GP*GP*AP*CP*CP*CP*AP*GP*AP*T)-3')


Mass: 3984.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: DNA chain DNA (5'-D(P*AP*AP*TP*CP*TP*GP*GP*GP*TP*CP*CP*TP*T)-3')


Mass: 3957.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: 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: 10120.914 Da / Num. of mol.: 2
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O95365
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→48.3 Å / Num. obs: 23116 / % possible obs: 100 % / Redundancy: 36 % / Biso Wilson estimate: 59.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.022 / Rrim(I) all: 0.133 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.27372.1374078311020.7320.352.1662.3100
9.07-48.323.60.09559732530.9940.0190.09733.499.3

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Processing

Software
NameVersionClassification
Aimless0.7.9data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EYI

7eyi


Resolution: 2.2→48.3 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1206 5.22 %
Rwork0.2239 21910 -
obs0.226 23116 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.04 Å2 / Biso mean: 83.6559 Å2 / Biso min: 38.45 Å2
Refinement stepCycle: final / Resolution: 2.2→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 530 4 23 1425
Biso mean--88.42 60.37 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.290.36991280.342724242552
2.29-2.390.35691390.290224362575
2.39-2.520.30021220.300924462568
2.52-2.680.42321140.348224642578
2.68-2.880.36841490.311624202569
2.88-3.170.29381610.270624132574
3.17-3.630.24931260.227424212547
3.63-4.580.24891210.177724622583
4.58-48.30.2081460.188624242570
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)
13.4237-1.8871.75944.86661.33689.2213-0.27450.0583-0.3461-0.41030.15480.44240.1869-0.47670.06680.62980.0279-0.06210.5449-0.14770.79274.447618.6573-6.9015
26.0242-1.10680.75674.3723-0.86226.96360.2355-0.28130.6149-0.0111-0.05411.4242-0.8157-0.9459-0.06680.620.0332-0.02290.6213-0.21250.81930.922418.6281-6.5193
34.8674-0.3131-1.32214.6158-3.01525.2745-0.0424-0.0268-0.0442-0.06330.129-0.03080.23750.0693-0.0780.39350.0352-0.01920.3482-0.08950.465211.78668.724-4.6282
49.2871-5.457-5.97463.71814.29956.1071-0.3493-0.70470.65240.85440.0676-0.03110.3942-0.71110.23620.57270.0792-0.04180.7322-0.24670.57252.186220.858.4338
58.4248-4.8665-1.83153.72882.56747.01440.3570.5510.0331-0.5539-0.2946-0.52590.64120.04420.02040.70390.11340.07510.7813-0.18670.9002-11.963330.2546-4.4341
69.6781-2.25821.89683.16823.76717.1654-0.96720.3220.2721-0.13781.0263-1.6114-0.93821.69720.30071.2332-0.17920.35491.2326-0.0961.625124.25546.724-2.4677
71.1601-1.39452.67946.6464-0.99937.1817-0.40860.30740.1425-0.32871.1876-1.15671.45162.7115-0.65611.213-0.2267-0.20472.0387-0.3711.556227.394114.0095-0.0044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 12 )A0 - 12
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 12 )B0 - 12
3X-RAY DIFFRACTION3chain 'G' and (resid 380 through 410 )G380 - 410
4X-RAY DIFFRACTION4chain 'G' and (resid 411 through 433 )G411 - 433
5X-RAY DIFFRACTION5chain 'G' and (resid 434 through 460 )G434 - 460
6X-RAY DIFFRACTION6chain 'F' and (resid 436 through 449 )F436 - 449
7X-RAY DIFFRACTION7chain 'F' and (resid 450 through 460 )F450 - 460

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