[English] 日本語
Yorodumi
- PDB-9dam: Crystal Structure of a DARPin Fused to the 1TEL Crystallization C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dam
TitleCrystal Structure of a DARPin Fused to the 1TEL Crystallization Chaperone via a Direct Helical Fusion in a 3-Fold Crystal Form
ComponentsTranscription factor ETV6 fused to a DARPin
KeywordsPROTEIN BINDING / TELSAM / DARPin / ETV6 / designed ankyrin 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 / DNA-binding transcription factor activity, RNA polymerase II-specific ...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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / 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
ACETIC ACID / Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsPedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E.W. / Nickles, R. ...Pedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E.W. / Nickles, R. / Doukov, T. / 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. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E.W. / Nickles, R. / Doukov, T. / Moody, J.D.
History
DepositionAug 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Structure summary / Category: struct / Item: _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor ETV6 fused to a DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3178
Polymers27,0791
Non-polymers2387
Water2,234124
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)83.290, 83.290, 58.434
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

-
Protein , 1 types, 1 molecules A

#1: Protein Transcription factor ETV6 fused to a DARPin


Mass: 27079.338 Da / Num. of mol.: 1
Fragment: residues 47-121 (Uniprot numbering) of the ETV6 portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ETV6, TEL, TEL1 / Plasmid: pET42_SUMO / Details (production host): kanamycin resistant / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): B / References: UniProt: P41212

-
Non-polymers , 5 types, 131 molecules

#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Description: Hexagonal prism, tapered to a point, round edges
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.6
Details: 1.0 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 6, 2024
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.78→45.4 Å / Num. obs: 22160 / % possible obs: 97.23 % / Redundancy: 21 % / Biso Wilson estimate: 30.93 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1516 / Rpim(I) all: 0.03361 / Rrim(I) all: 0.1553 / Net I/σ(I): 14.13
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 20.2 % / Rmerge(I) obs: 5.909 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1639 / CC1/2: 0.335 / CC star: 0.708 / Rpim(I) all: 1.332 / Rrim(I) all: 6.06 / % possible all: 75.01

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→45.4 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 1061 4.89 %
Rwork0.2045 20631 -
obs0.2053 21692 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 10 124 1909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01191831
X-RAY DIFFRACTIONf_angle_d1.02032500
X-RAY DIFFRACTIONf_chiral_restr0.0582285
X-RAY DIFFRACTIONf_plane_restr0.0054331
X-RAY DIFFRACTIONf_dihedral_angle_d13.0391625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.860.37011050.32832038X-RAY DIFFRACTION76.95
1.86-1.950.31411280.29422645X-RAY DIFFRACTION99.86
1.95-2.080.24241280.24962663X-RAY DIFFRACTION100
2.08-2.240.22651340.22632635X-RAY DIFFRACTION99.89
2.24-2.460.25221560.21352632X-RAY DIFFRACTION100
2.46-2.820.2241470.20482640X-RAY DIFFRACTION99.01
2.82-3.550.21291250.19662663X-RAY DIFFRACTION99.96
3.55-45.40.19191380.17992715X-RAY DIFFRACTION99.3

+
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