[English] 日本語
Yorodumi
- PDB-9cpl: The ubiquitin-associated domain of human thirty-eight negative ki... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cpl
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker
Components2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein
KeywordsONCOPROTEIN / TELSAM / 2TEL / Pointed Domain / ETS / TEL / TNK1 / UBA Domain / Broken Periodicity
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 / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / DNA-binding transcription repressor 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 / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / protein autophosphorylation / protein tyrosine kinase activity / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein phosphorylation / 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 / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / SAM domain-like / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family ...: / : / SAM domain-like / 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 / Src homology 3 domains / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Transcription factor ETV6 / Non-receptor tyrosine-protein kinase TNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSamarawickrama, P. / Averett, J. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209-01 United States
CitationJournal: To Be Published
Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons
Authors: Samarawickrama, P. / Ludlow, K. / Probst, R. / Abiodun, W. / Averett, J. / Hansen, D. / Doukov, T. / Moody, J.D.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1392
Polymers29,0931
Non-polymers461
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.725, 105.725, 50.917
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 2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein


Mass: 29092.832 Da / Num. of mol.: 1
Mutation: First TELSAM:R80S,V112E,Second TELSAM: R80S,UBA Domain: C610A,C644A
Source method: isolated from a genetically manipulated source
Details: Tandem fusion of Two TELSAM Domains followed by TNK1 domain
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42-His-2TEL-XhoI / Details (production host): N-term 10xHis / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.48 % / Description: clusters of rice-shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100mM BisTris, pH 6.0, 960mM Mg-formate

-
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: Aug 25, 2023 / Details: Rh coated collimating mirror, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, 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: 2.4→45.78 Å / Num. obs: 12862 / % possible obs: 99.12 % / Redundancy: 10.2 % / Biso Wilson estimate: 68.73 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1028 / Rpim(I) all: 0.03386 / Rrim(I) all: 0.1083 / Net I/σ(I): 10.88
Reflection shellResolution: 2.4→2.4 Å / Redundancy: 10.2 % / Rmerge(I) obs: 3.597 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 1150 / CC1/2: 0.449 / CC star: 0.787 / Rpim(I) all: 1.173 / Rrim(I) all: 3.786 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.78 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2634 713 5.58 %
Rwork0.2294 12070 -
obs0.2313 12783 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 3 17 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341841
X-RAY DIFFRACTIONf_angle_d0.48012504
X-RAY DIFFRACTIONf_chiral_restr0.0369272
X-RAY DIFFRACTIONf_plane_restr0.0041317
X-RAY DIFFRACTIONf_dihedral_angle_d10.77641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.580.36421580.35432277X-RAY DIFFRACTION94.71
2.58-2.840.38481520.29912397X-RAY DIFFRACTION99.96
2.84-3.250.37881400.32412434X-RAY DIFFRACTION99.96
3.25-4.10.25981120.23542466X-RAY DIFFRACTION100
4.1-45.780.21361510.1832496X-RAY DIFFRACTION99.77
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)
17.34509794456-2.21562849081-6.101102956490.9943870603942.410123543096.049122618160.2200014744390.479795485913-0.945008722505-0.439925333384-0.4829353522580.190043785899-0.703964678376-0.5179569732640.1440114104250.697586773690.03993628586890.02281794518440.6438256484090.05512686827360.617184102158-31.08123977-20.1639401076-12.5180262115
25.3273440286-0.798351291842-3.630961825932.503241341020.6101304121446.45070281090.3890267462110.945503290588-0.415875209572-0.266391160893-0.26601361501-0.176464236512-0.482649177580.197935700209-0.04831104111750.7112534626740.1836302048770.03566208531240.7758567565950.05318518243520.550291603516-12.3001554273-26.3216557561-31.3219425066
38.94524801384-1.470218191390.6136455046664.83486141045-1.633136585255.81621788532-0.126967850266-0.168327745045-0.03122320771170.04358634998490.2003349882070.261469058046-0.509781466358-0.257297388823-0.01809016992650.5863601033690.00927879790659-0.05635180423340.378025746475-0.01927109908760.475331134584-52.919820658-8.98365557114-7.63946223226
47.469938518070.0734209488661-0.4261938639724.1546064027-1.240554830483.75947465187-0.297092882727-1.16847820802-0.6005474009660.415561069073-0.481632820546-0.664745675293-0.1538944418591.324229619590.7381288888630.539102287531-0.0605047632494-0.003508386002420.886131320920.2581209097340.60398023791-34.6067489737-18.30202282690.812853101302
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 161 through 186 )161 - 186144 - 169
22chain 'A' and (resid 187 through 251 )187 - 251170 - 234
33chain 'A' and (resid 14 through 87 )14 - 871 - 74
44chain 'A' and (resid 88 through 160 )88 - 16075 - 143

+
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