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- PDB-7eyi: Crystal structure of ZBTB7A in complex with gamma-globin -200 seq... -

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Basic information

Entry
Database: PDB / ID: 7eyi
TitleCrystal structure of ZBTB7A in complex with gamma-globin -200 sequence element with C-194A mutation
Components
  • DNA (5'-D(*AP*TP*AP*GP*GP*GP*CP*CP*CP*CP*TP*TP*CP*CP*CP*AP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*TP*GP*GP*GP*AP*AP*GP*GP*GP*GP*CP*CP*CP*TP*A)-3')
  • Zinc finger and BTB domain-containing protein 7A
KeywordsSTRUCTURAL PROTEIN / ZBTB7A / gamma-globin / -200 cluste.
Function / homology
Function and homology information


regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / 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 / negative regulation of Notch signaling pathway / fat cell differentiation ...regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / 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 / negative regulation of Notch signaling pathway / fat cell differentiation / erythrocyte maturation / SMAD binding / regulation of alternative mRNA splicing, via spliceosome / 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 / chromatin organization / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / 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 / nucleus / metal ion binding / 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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
BORIC ACID / DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.401 Å
AuthorsYang, Y. / Shi, Y.Y.
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
DepositionMay 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 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_author.identifier_ORCID / _citation_author.name
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Zinc finger and BTB domain-containing protein 7A
H: Zinc finger and BTB domain-containing protein 7A
A: DNA (5'-D(*AP*TP*AP*GP*GP*GP*CP*CP*CP*CP*TP*TP*CP*CP*CP*AP*AP*C)-3')
B: DNA (5'-D(*TP*GP*TP*TP*GP*GP*GP*AP*AP*GP*GP*GP*GP*CP*CP*CP*TP*A)-3')
C: DNA (5'-D(*AP*TP*AP*GP*GP*GP*CP*CP*CP*CP*TP*TP*CP*CP*CP*AP*AP*C)-3')
D: DNA (5'-D(*TP*GP*TP*TP*GP*GP*GP*AP*AP*GP*GP*GP*GP*CP*CP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,87715
Polymers52,2926
Non-polymers5859
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.440, 67.440, 228.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules GH

#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: 15111.705 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

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DNA chain , 2 types, 4 molecules ACBD

#2: DNA chain DNA (5'-D(*AP*TP*AP*GP*GP*GP*CP*CP*CP*CP*TP*TP*CP*CP*CP*AP*AP*C)-3')


Mass: 5421.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*GP*TP*TP*GP*GP*GP*AP*AP*GP*GP*GP*GP*CP*CP*CP*TP*A)-3')


Mass: 5612.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 38 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M MIB buffer,pH 7.0, 25% (w/v) polyethylene glycol (PEG) 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 19866 / % possible obs: 99.1 % / Redundancy: 25.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 36.9
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 1.382 / Num. unique obs: 1029

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.401→33.72 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 1029 5.18 %
Rwork0.2221 18837 -
obs0.2244 19866 92.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.94 Å2 / Biso mean: 48.4965 Å2 / Biso min: 10.92 Å2
Refinement stepCycle: final / Resolution: 2.401→33.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 1394 12 29 3251
Biso mean--43.3 31.29 -
Num. residues----291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4013-2.52790.3722960.3304170560
2.5279-2.68620.37131440.3295255490
2.6862-2.89350.38411520.3018283699
2.8935-3.18450.30841680.2829286299
3.1845-3.64480.27371680.2131283699
3.6448-4.59020.22091420.18112970100
4.5902-8.50.19561590.1736307498
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)
17.4929-0.21362.9873.111-1.26876.0131-0.0672-0.1137-0.08670.22540.25790.06090.15350.0503-0.15520.34920.00070.08790.18850.0550.19842.651751.316431.0304
20.31190.8268-0.4672.1839-1.30171.6618-0.13940.08210.52290.10340.53880.7412-0.1732-0.5487-0.18050.2867-0.02130.11760.22110.14490.471-1.857865.725623.7459
33.21961.6867-1.45682.2357-0.86091.7891-0.0947-0.189-0.2309-0.28870.2230.03690.00630.0572-0.16790.3836-0.07190.06240.09570.07080.349111.996878.23515.7576
43.2249-1.0457-1.55151.12331.52042.0666-0.1412-0.2705-0.2760.53340.48530.4983-0.1727-0.2276-0.30720.5187-0.02290.14870.26790.11560.423324.591272.171414.5731
54.54981.8645-0.36963.6811-0.24424.7965-0.04410.0602-1.089-0.02010.1511-0.78990.59840.5358-0.09360.37750.07840.07070.34780.0340.534329.62857.772311.2121
68.89195.20164.08793.30841.57824.44910.15520.6037-0.9248-0.53180.109-0.44880.58250.3067-0.25580.44730.02980.1030.35660.05330.478321.721452.14869.0001
78.65592.6712-2.17645.82851.50297.74110.024-0.40080.01820.63970.1927-0.09190.25920.02210.03480.47510.0929-0.15320.2375-0.09630.164817.439648.494231.9055
80.17940.32210.0392.05071.06671.0617-0.2086-0.0758-0.07130.28380.4462-0.50340.39920.3694-0.13710.25650.0122-0.0561-0.0143-0.18570.180220.441932.707720.6904
92.0942-0.5113-0.4952.65810.46976.34440.22460.07720.01140.0545-0.14660.2654-0.4139-0.97650.02810.5109-0.11750.08690.264-0.00790.1515-0.33525.94139.991
102.9061-2.1087-0.4843.90362.98885.15680.0707-0.15420.8218-0.5352-0.08350.8012-1.1273-0.89590.14170.83330.09150.02520.627-0.07041.2455-8.357545.08067.5273
111.9094-0.87140.65127.48510.15355.7948-0.44040.38010.8448-0.9794-0.16641.058-0.9365-0.93510.42360.83590.1336-0.21060.71230.02520.6851-1.341546.27156.1638
127.31541.6842-2.92853.96331.59014.8546-0.25231.00631.3102-1.21570.18310.2173-1.3197-0.25120.10111.0894-0.0687-0.02660.8604-0.16331.12540.982456.49984.9652
132.77472.5518-3.27388.9215-4.41537.99290.1864-1.06180.39972.2154-0.29611.1038-0.8164-0.61360.05881.01840.01170.18750.668-0.250.75475.206569.423335.6818
147.81162.6465-0.90843.27022.42585.1282-0.17490.11910.11250.5855-0.0624-0.89960.1010.45340.20840.4940.0188-0.00660.28940.16220.484315.60364.901521.092
152.0296-0.0213-1.93195.1568-1.01066.337-0.18541.12580.0986-0.89120.64810.03110.7645-1.2839-0.36220.4391-0.07280.0890.61920.06530.328413.165863.07762.3359
163.33740.19510.70272.9482-2.12882.7956-0.19850.6520.0334-0.42390.2791-0.12640.1383-0.20150.28150.6045-0.05690.25030.33340.09110.303420.685963.873.5636
173.29731.1696-1.16590.9386-0.79892.12260.16350.63570.4585-0.09950.03870.0122-0.2895-0.6737-0.10240.42380.03830.22440.47130.11210.33217.67163.988416.7345
182.46380.3182-0.37531.54361.89112.56240.0827-1.12080.75071.0999-0.2451-0.487-0.4255-0.1106-0.12890.9097-0.0491-0.03740.3604-0.20150.567513.531767.128433.9348
196.9418-4.03442.96275.3127-0.11695.04940.0511-0.60381.35280.36380.0119-0.5508-0.68380.1409-0.04881.65360.1014-0.10491.1481-0.53551.53568.194976.18142.3445
200.9692-0.61061.05490.4773-0.38782.1586-0.0642-0.5556-0.14720.5352-0.0174-0.0180.1142-0.0138-0.1160.8272-0.16480.01540.58430.1321-0.044210.033532.142132.4672
212.26341.3332-0.37781.46651.06275.41330.37160.52190.021-0.16290.2605-0.0911-0.4980.3842-0.21850.4782-0.0484-0.15440.37150.0120.18679.85542.11583.8078
221.63440.08660.35210.101-0.02291.9447-0.01040.39470.0584-0.40140.05250.1893-0.0189-0.25140.10430.83790.058-0.33990.57790.0519-0.05778.305940.71783.8541
233.09640.5223-0.3163.2222-2.74132.3407-0.1033-0.7947-0.23860.17790.14320.14530.6533-0.3732-0.15560.7475-0.052-0.01250.42640.07080.15518.122832.340332.1851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 380 through 389 )G380 - 389
2X-RAY DIFFRACTION2chain 'G' and (resid 390 through 421 )G390 - 421
3X-RAY DIFFRACTION3chain 'G' and (resid 422 through 449 )G422 - 449
4X-RAY DIFFRACTION4chain 'G' and (resid 450 through 461 )G450 - 461
5X-RAY DIFFRACTION5chain 'G' and (resid 462 through 477 )G462 - 477
6X-RAY DIFFRACTION6chain 'G' and (resid 478 through 490 )G478 - 490
7X-RAY DIFFRACTION7chain 'H' and (resid 379 through 389 )H379 - 389
8X-RAY DIFFRACTION8chain 'H' and (resid 390 through 433 )H390 - 433
9X-RAY DIFFRACTION9chain 'H' and (resid 434 through 461 )H434 - 461
10X-RAY DIFFRACTION10chain 'H' and (resid 462 through 471 )H462 - 471
11X-RAY DIFFRACTION11chain 'H' and (resid 472 through 484 )H472 - 484
12X-RAY DIFFRACTION12chain 'H' and (resid 485 through 490 )H485 - 490
13X-RAY DIFFRACTION13chain 'A' and (resid -207 through -203 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid -202 through -198 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid -197 through -192 )A0
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 5 )B1 - 5
17X-RAY DIFFRACTION17chain 'B' and (resid 6 through 10 )B6 - 10
18X-RAY DIFFRACTION18chain 'B' and (resid 11 through 15 )B11 - 15
19X-RAY DIFFRACTION19chain 'B' and (resid 16 through 16 )B16
20X-RAY DIFFRACTION20chain 'C' and (resid -209 through -200 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid -199 through -192 )C0
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 10 )D1 - 10
23X-RAY DIFFRACTION23chain 'D' and (resid 11 through 18 )D11 - 18

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