[English] 日本語
Yorodumi
- PDB-9dp8: A DARPin fused to the 1TEL crystallization chaperone via a helica... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dp8
TitleA DARPin fused to the 1TEL crystallization chaperone via a helical Lys-Gln-Arg linker
ComponentsTranscription Factor ETV6, DARPin fusion
KeywordsPROTEIN BINDING / TELSAM / DARPin / ETV6 / Designed Ankryn Repeat Protein
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsPedroza Romo, M.J. / Keliiliki, A.C. / Noakes, E. / Averett, B. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209 United States
CitationJournal: To Be Published
Title: Optimal TELSAM-Target Protein Linker Character is Target Protein Dependent.
Authors: Pedroza Romo, M.J. / Averett, J.C. / Keliiliki, A.C. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J.F. / Noakes, E. / Nickles, R. / Doukov, T. / Moody, J.D.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription Factor ETV6, DARPin fusion


Theoretical massNumber of molelcules
Total (without water)27,5391
Polymers27,5391
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.981, 105.981, 51.137
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Transcription Factor ETV6, DARPin fusion / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 27538.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.14 % / Description: "Feather"
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 0.3 M Magnesium formate dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.47→45.89 Å / Num. obs: 3961 / % possible obs: 87.47 % / Redundancy: 9.4 % / Biso Wilson estimate: 147.09 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1269 / Rpim(I) all: 0.04332 / Rrim(I) all: 0.1343 / Net I/σ(I): 7.03
Reflection shellResolution: 3.474→3.598 Å / Redundancy: 9.2 % / Rmerge(I) obs: 3.2 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 320 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 1.111 / Rrim(I) all: 3.39 / % possible all: 75.29

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot1.20.1_4487model building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.47→45.89 Å / SU ML: 0.4002 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2979 190 4.99 %
Rwork0.2708 3618 -
obs0.272 3808 87.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 230.13 Å2
Refinement stepCycle: LAST / Resolution: 3.47→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 0 1 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371672
X-RAY DIFFRACTIONf_angle_d0.63942291
X-RAY DIFFRACTIONf_chiral_restr0.0346267
X-RAY DIFFRACTIONf_plane_restr0.004310
X-RAY DIFFRACTIONf_dihedral_angle_d12.459549
LS refinement shellResolution: 3.47→45.89 Å
RfactorNum. reflection% reflection
Rfree0.2979 190 -
Rwork0.2708 3618 -
obs--87.26 %
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)
15.83822787567-3.946962127970.5462735818165.913526909143.139606170547.800871696510.4286261662760.86785855029-0.893722974816-1.13360736838-0.526898581370.8197130530121.13873322333-2.332019734710.3423578600961.02915218884-0.376242892549-0.1027418281341.30368460706-0.1245065084650.868914249592-15.783630491-14.8424769926-8.41041887019
25.531920665163.16339809158-3.217017813198.24021482309-3.299600444979.20303144026-0.0670085209211-1.72871081358-2.301158515353.00691134329-0.1109240299051.052281446970.38215272875-1.13323093458-0.5541291184362.15760771576-0.220304249360.2588741163171.872242490550.5030605343271.88447289869-20.1128217133-23.397800932814.254108576
33.3213391979-1.70887316632-0.791685936623.85052212786-2.045506233075.39836929328-1.610330440260.543130366302-1.124392536362.436624785762.457404178832.955960355971.80248639734-2.33190500466-0.2857836730533.49479549887-1.632560219770.1618903127432.783181459190.6938242751174.2431350019-34.4268511306-36.01073992116.4779192526
41.223042318951.697159864130.2991277810275.74580433426-2.122587787641.93776075688-0.7148927086370.48203074189-1.4757268855-0.05678508142790.5828276219121.50405137770.76833077136-0.4766338827281.681831536373.70609943731-1.832144660940.3814081265384.291370828251.5388828423.59747611972-38.5865886778-43.968093895122.5969026319
55.90066650133-3.13185044137-5.000779425391.66051292272.476250431176.153424164590.60166929012.92032997315-0.729620244784-1.4968762373-0.5573910785083.25743625266-0.761487005211-3.251932745060.1293990500474.14874215146-2.40866066844-0.7369191430642.835305611030.07013045020384.51957629213-40.5823476152-52.282463980917.419357508
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 77 )16 - 771 - 62
22chain 'A' and (resid 78 through 149 )78 - 14963 - 134
33chain 'A' and (resid 150 through 195 )150 - 195135 - 180
44chain 'A' and (resid 196 through 215 )196 - 215181 - 200
55chain 'A' and (resid 216 through 248 )216 - 248201 - 233

+
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