[English] 日本語
Yorodumi
- PDB-7n5s: ZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Prom... -

+
Open data


ID or keywords:

Loading...

-
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 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: 2.86 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more