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- PDB-7n5s: ZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Prom... -

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Basic information

Entry
Database: PDB / ID: 7n5s
TitleZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Promoter (Oligo 6)
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 / histone acetyltransferase binding / regulation of alternative mRNA splicing, via spliceosome / erythrocyte maturation ...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 / histone acetyltransferase binding / regulation of alternative mRNA splicing, via spliceosome / erythrocyte maturation / 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 / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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: 2.86 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)26,0837
Polymers25,8213
Non-polymers2624
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-30 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.938, 36.963, 74.257
Angle α, β, γ (deg.)90.000, 100.012, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

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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: 4676.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand II


Mass: 4506.912 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME

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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: 2.85→36.32 Å / Num. obs: 10160 / % possible obs: 92.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 107.27 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Net I/σ(I): 18.8
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 628 / CC1/2: 0.61 / Rpim(I) all: 0.701 / % possible all: 66

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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: 2.86→36.32 Å / SU ML: 0.4711 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 501 4.95 %
Rwork0.226 9623 -
obs0.2283 10124 89.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.55 Å2
Refinement stepCycle: LAST / Resolution: 2.86→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 577 4 1 1415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251499
X-RAY DIFFRACTIONf_angle_d0.42682144
X-RAY DIFFRACTIONf_chiral_restr0.0318231
X-RAY DIFFRACTIONf_plane_restr0.0026182
X-RAY DIFFRACTIONf_dihedral_angle_d22.6371581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.150.5154980.46061805X-RAY DIFFRACTION67.7
3.15-3.60.42851310.30592526X-RAY DIFFRACTION93.03
3.6-4.540.26761410.25292676X-RAY DIFFRACTION99.4
4.54-36.320.2231310.17862616X-RAY DIFFRACTION96.39
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)
15.73799415741-3.915206219710.9061663914096.33492709643-0.463368902637.965723007870.6921900509071.507791544340.8450680312270.4199322480040.3727381458350.553476678573-1.911504987361.10268445104-0.9167165004530.734018769965-0.1870949237570.2820233084980.84051500680.01891638286540.74918747913-5.5665354466210.513919632728.2108670132
27.20299587791-0.43390394217-4.2095062342910.0822085016-0.238384117486.35227325825-0.732967911545-0.756152051851-0.7838550039890.06963475297121.48864813501-1.025762837180.2915756285940.0525691851652-0.7965128028990.5292776425380.149582453510.08629364446870.744006658709-0.08546082618180.8837062417711.10132475404-8.1728475215532.5026235528
34.131534074113.59790518502-0.1882246661353.76875737047-0.6165229827991.09635337917-0.4475736207221.143186188-0.1692754764510.0001040372399470.888175687210.167550847230.620708065419-0.52516211331-0.5706827193781.32242171217-0.1956937682270.589371474671.41687422739-0.3432607869461.27283165029.98119246384-11.818467246110.9700800959
46.491599664613.713170885886.475330443047.241592225296.490272818157.994330767961.333953118295.498113249220.487673733399-0.4125577115970.1246229407080.617861517537-3.220393501220.460581429399-1.474524208511.802327626051.008563301210.1537541545231.98441429858-0.0895560216380.8428515607518.98039682667.785620048535.19377590023
54.711405971125.52996323212-3.643890088739.26090876537-1.766014078174.9855372924-0.207546010441-0.3254539077012.3268554262.273094438741.368987650571.27201196317-0.8019377243940.00750692549793-1.515082730380.635276113926-0.03366637375560.4889343508641.230922789760.2431375634091.4218966025321.04408437543.995995941818.82448957949
63.180842654392.24552033506-0.9650484976864.36395162194-3.852400342433.952812276670.4578490672511.886272344222.321633913341.783363625380.8276777925830.981085226958-2.90579882398-2.0600753985-0.5702473104661.76912345830.01370532303440.1499170676761.365063197330.04448141585131.2200149721120.24826581379.8254789131613.9999966844
74.13192231647-2.982244104381.161571523715.44855669281-3.762197957237.63600035714-0.8047949859940.539740410056-1.63882892984-0.5198685134820.5817419556580.345345587650.910574626519-0.2858208636470.319126945750.791964880934-0.25050923020.1506542817841.30092647367-0.1162021877290.9451597459055.38983734064-0.21601548177920.2131482065
83.471856056725.6859058102-0.2572347407129.56252418788-0.2419144142139.64327324517-0.967345270874-0.4378219615930.83607781737-0.3037422348470.3630976660680.407848261017-0.0774198435496-0.2694292084490.5769015555540.775008473525-0.06942624336270.01989021350911.14493336987-0.1967477428340.7088339792182.551840314610.065373430517522.5729315506
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 404 )AA381 - 4041 - 24
22chain 'A' and (resid 405 through 433 )AA405 - 43325 - 53
33chain 'A' and (resid 434 through 465 )AA434 - 46554 - 85
44chain 'A' and (resid 466 through 470 )AA466 - 47086 - 90
55chain 'A' and (resid 471 through 477 )AA471 - 47791 - 97
66chain 'A' and (resid 478 through 491 )AA478 - 49198 - 111
77chain 'X' and (resid 2 through 15 )XF2 - 15
88chain 'Y' and (resid 0 through 14 )YG0 - 14

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