[English] 日本語
Yorodumi
- PDB-7n2b: A DARPin semi-rigidly fused to the 3TEL crystallization chaperone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n2b
TitleA DARPin semi-rigidly fused to the 3TEL crystallization chaperone
ComponentsTranscription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin
KeywordsPROTEIN BINDING / Designed Ankyrin repeat protein / Translocation ETS Leukemia / Sterile Alpha Motif / polymer
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / 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 / Signaling by FLT3 fusion proteins / neurogenesis / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / 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 family / Ets-domain signature 2. / Ets domain / 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 family / Ets-domain signature 2. / Ets domain / 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: 3.221 Å
AuthorsSarath Nawarathange, S.D. / Gajjar, P. / Bunn, D. / Stewart, C. / Doukov, T. / Moody, J.D.
CitationJournal: Open Biology / Year: 2022
Title: Crystals of TELSAM-target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts.
Authors: Nawarathnage, S. / Soleimani, S. / Mathis, M.H. / Bezzant, B.D. / Ramirez, D.T. / Gajjar, P. / Bunn, D.R. / Stewart, C. / Smith, T. / Pedroza Romo, M.J. / Brown, S. / Doukov, T. / Moody, J.D.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 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: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin
B: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin


Theoretical massNumber of molelcules
Total (without water)93,6352
Polymers93,6352
Non-polymers00
Water00
1
A: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin


Theoretical massNumber of molelcules
Total (without water)46,8181
Polymers46,8181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin


Theoretical massNumber of molelcules
Total (without water)46,8181
Polymers46,8181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.962, 63.625, 166.005
Angle α, β, γ (deg.)90.000, 90.162, 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

-
Components

#1: Protein Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 46817.559 Da / Num. of mol.: 2 / Mutation: V67E
Source method: isolated from a genetically manipulated source
Details: the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the ...Details: the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 % / Description: Thin circular or half-moon plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 mM L-Proline, 100 mM HEPES, 10 % w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.221→40.16 Å / Num. obs: 13842 / % possible obs: 87.26 % / Redundancy: 3.3 % / Biso Wilson estimate: 84.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07087 / Rrim(I) all: 0.08449 / Net I/σ(I): 10.98
Reflection shellResolution: 3.221→3.336 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5057 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 1491 / CC1/2: 0.906 / CC star: 0.975 / Rpim(I) all: 0.3275 / Rrim(I) all: 0.6052 / % possible all: 95.36

-
Processing

Software
NameVersionClassification
Coot0.9model building
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QAR, 4J7W

2qar

4j7w


Resolution: 3.221→40.16 Å / SU ML: 0.4014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The dataset was initially scaled into space group P212121 and phased with 1 molecule in the AU, but scaling into space group P1211 and phasing with 2 molecules in the AU gave superior refinement statistics.
RfactorNum. reflection% reflection
Rfree0.2425 681 4.94 %
Rwork0.2264 13096 -
obs0.2273 13777 87.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.51 Å2
Refinement stepCycle: LAST / Resolution: 3.221→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 0 0 6067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336206
X-RAY DIFFRACTIONf_angle_d0.56258483
X-RAY DIFFRACTIONf_chiral_restr0.0393968
X-RAY DIFFRACTIONf_plane_restr0.00541113
X-RAY DIFFRACTIONf_dihedral_angle_d11.14072121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.470.37591090.31662252X-RAY DIFFRACTION75.97
3.47-3.820.33951230.27492510X-RAY DIFFRACTION83.8
3.82-4.370.24381340.22372493X-RAY DIFFRACTION84.01
4.37-5.50.24081510.22992860X-RAY DIFFRACTION95.74
5.51-41.750.19131640.19372981X-RAY DIFFRACTION96.74
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)
12.343110453510.8747071844482.353412656843.685569858781.126259039845.586139399480.394434583743-0.270691619816-0.1129852870080.545903512559-0.315510108311-0.01432345372670.592126477484-0.281179680064-0.0566553205020.718893871115-0.04096230743410.1086167165340.4300467147360.0145081254540.601491645224-4.44310941214-6.0537924262850.7038023555
24.63416247747-2.20469977267-3.992071401920.4501470619141.641584712941.348258041740.2147120830060.108109657594-0.356566551174-0.140888834444-0.562438226999-0.0393419058333-0.5137921393450.2978709528190.2813630653741.067757288990.0683085266355-0.06381920523450.832247622344-0.03260767620550.7521899112018.82543759353-17.062002471516.5033754056
38.26542474682-4.58505616156-2.070582464348.456926754591.939089311053.41449007877-0.471169086585-0.01008594970970.1461967249960.488763993720.334219998982-1.262814193810.2948478286140.2613483883550.134757092840.98712417674-0.02553416141280.002292989802250.5071836977420.07595599225670.69385663322436.4366811554-30.44185433766.01960821407
43.20600649914-1.63710827058-4.280803260463.993656746842.583400274189.288030724480.290374234430.2138622673670.0666526469764-0.225801638489-0.3078617163320.167972392642-0.453451687104-0.237953105791-0.02124736268750.551942870877-0.0106815741115-0.1502223541390.3891571494460.02621720937050.499555363358-27.401654364418.746589952932.3174531534
55.644229372572.392090973544.425968377870.4020022262541.430055592563.196976159940.393070795934-0.4904197252270.2828790229580.229207792551-0.613100681254-0.05044343618360.478387564914-0.163713437494-0.1517994432691.08495801129-0.08980458976060.02842225298860.736959848435-0.02641914017960.810299776159-14.021846700229.812382650266.8526969711
68.001502241063.116185310582.493910416096.384950020470.5705754712063.81353613852-0.7531039710030.110417006882-0.0533600026222-1.086338787280.552545061267-1.39837897472-0.6871674010010.1923259628860.2126991956871.13426818366-0.03229477962940.04587144096890.527017244247-0.02103254209910.73847303940513.215973018243.038405231277.1971848273
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 233 )AA1 - 2331 - 220
22chain 'A' and (resid 234 through 295 )AA234 - 295221 - 282
33chain 'A' and (resid 296 through 415 )AA296 - 415283 - 402
44chain 'B' and (resid 1 through 233 )BB1 - 2331 - 223
55chain 'B' and (resid 234 through 295 )BB234 - 295224 - 285
66chain 'B' and (resid 296 through 414 )BB296 - 414286 - 404

+
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://pdbjlvh1.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