[English] 日本語
Yorodumi
- PDB-8ufz: Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG) in T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ufz
TitleHuman PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG) in Ternary Complex with DB1976
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
  • Transcription factor PU.1
KeywordsTRANSCRIPTION / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex / diamidine / minor-groove binder / transcription inhibition
Function / homology
Function and homology information


positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / TRAIL-activated apoptotic signaling pathway / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation ...positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / TRAIL-activated apoptotic signaling pathway / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / defense response to tumor cell / oncogene-induced cell senescence / regulation of DNA-binding transcription factor activity / positive regulation of p38MAPK cascade / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein localization to chromatin / positive regulation of B cell differentiation / DNA-binding transcription repressor activity / STAT family protein binding / DNA-binding transcription activator activity / interleukin-6-mediated signaling pathway / NFAT protein binding / negative regulation of NF-kappaB transcription factor activity / cis-regulatory region sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / protein sequestering activity / regulation of erythrocyte differentiation / positive regulation of miRNA transcription / histone deacetylase binding / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Transcription factor PU.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsTerrell, J.R. / Poon, G.M.K. / Wilson, W.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
National Science Foundation (NSF, United States)MCB2028902 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137160 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
CitationJournal: To Be Published
Title: Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders
Authors: Terrell, J.R. / Paul, A. / Ogbonna, E.N. / Farahat, A.A. / Poon, G.M.K. / Wilson, W.D.
History
DepositionOct 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
B: DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
E: Transcription factor PU.1
F: Transcription factor PU.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3578
Polymers44,4626
Non-polymers8952
Water00
1
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
B: DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
F: Transcription factor PU.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6784
Polymers22,2313
Non-polymers4471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')
E: Transcription factor PU.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6784
Polymers22,2313
Non-polymers4471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.375, 74.446, 58.097
Angle α, β, γ (deg.)90.000, 113.837, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "C" and resid 1 through 16)
d_1ens_2(chain "B" and resid 17 through 32)
d_2ens_2chain "D"
d_1ens_3(chain "E" and (resid 169 through 211 or resid 213...
d_2ens_3(chain "F" and (resid 169 through 203 or (resid 204...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1DADADGDGAA1 - 81 - 8
d_21ens_1DADADGDGCC1 - 81 - 8
d_11ens_2DTDTDTDTBB171
d_21ens_2DTDTDTDTDD171
d_11ens_3LYSLYSHISHISEE169 - 2115 - 47
d_12ens_3TRPTRPGLYGLYEE213 - 25849 - 94
d_21ens_3LYSLYSHISHISFF169 - 2115 - 47
d_22ens_3TRPTRPGLYGLYFF213 - 25849 - 94

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.481330376958, 0.0654643890686, 0.87409123207), (-0.0287215085145, -0.995493778018, 0.0903726334521), (0.876068572183, -0.0686043124905, -0.477281159424)-0.4713956089, -21.1190908452, 8.29760053585
2given(0.483186927513, 0.0796146441198, 0.871889844833), (-0.0280133929205, -0.993941121474, 0.106284038593), (0.875068936083, -0.0757796508579, -0.478029080306)-0.429687164958, -20.8894136195, 8.08330783081
3given(0.486816628082, 0.0293002129987, 0.873012639164), (0.123630994547, -0.991687430022, -0.0356569533679), (0.864710904181, 0.125289818639, -0.486392345268)-6.82460911173, -21.4944833837, 6.95298568369

-
Components

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


Mass: 5004.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*TP*TP*AP*T)-3')


Mass: 4790.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor PU.1 / 31 kDa-transforming protein


Mass: 12436.583 Da / Num. of mol.: 2 / Fragment: ETS-Domain UNP residues 165-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P17947
#4: Chemical ChemComp-Y5U / (2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)


Mass: 447.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N8Se / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex - Ligand incorporated via soaking at 500uM concentration 24h

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.920119 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationMonochromator: Horizontal double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920119 Å / Relative weight: 1
ReflectionResolution: 3.06→29.29 Å / Num. obs: 8196 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 96.42 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.052 / Rrim(I) all: 0.109 / Net I/σ(I): 7
Reflection shellResolution: 3.06→3.27 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1485 / CC1/2: 0.982 / Rpim(I) all: 0.138 / Rrim(I) all: 0.29 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→29.29 Å / SU ML: 0.485 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.6066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 783 9.93 %
Rwork0.257 7106 -
obs0.2598 7889 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.32 Å2
Refinement stepCycle: LAST / Resolution: 3.06→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 984 58 0 2837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383040
X-RAY DIFFRACTIONf_angle_d0.80844363
X-RAY DIFFRACTIONf_chiral_restr0.0379458
X-RAY DIFFRACTIONf_plane_restr0.0021326
X-RAY DIFFRACTIONf_dihedral_angle_d23.58561253
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.708011681404
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.749317820453
ens_3d_2EEX-RAY DIFFRACTIONTorsion NCS0.625516231388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.250.41841210.40641135X-RAY DIFFRACTION91.61
3.25-3.50.33891250.38691104X-RAY DIFFRACTION90.84
3.5-3.850.37511260.32861173X-RAY DIFFRACTION95.03
3.85-4.410.35021280.27131216X-RAY DIFFRACTION97.82
4.41-5.550.27541440.27031225X-RAY DIFFRACTION99.27
5.56-29.290.22351390.18741253X-RAY DIFFRACTION99.5
Refinement TLS params.Method: refined / Origin x: 6.92607035312 Å / Origin y: -11.1667559612 Å / Origin z: 9.08817809415 Å
111213212223313233
T0.774477961322 Å2-0.196986811055 Å2-0.484014956613 Å2-1.60830357362 Å20.208322142095 Å2--0.705356990164 Å2
L2.06721943522 °2-2.09918621641 °2-2.50112617427 °2-0.77420470679 °21.61133923085 °2--3.00997293796 °2
S-0.167212328984 Å °0.53511113513 Å °-0.131215435719 Å °-0.0366915531795 Å °0.123779813668 Å °0.532568925784 Å °-0.0763993279734 Å °-0.0180991793949 Å °-0.109183889325 Å °
Refinement TLS groupSelection details: all

+
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