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- PDB-7y62: Crystal structure of human TFEB HLHLZ domain -

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Basic information

Entry
Database: PDB / ID: 7y62
TitleCrystal structure of human TFEB HLHLZ domain
ComponentsTranscription factor EB
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


antibacterial innate immune response / lysosome localization / lysosome organization / humoral immune response / Transcriptional and post-translational regulation of MITF-M expression and activity / embryonic placenta development / positive regulation of autophagy / cellular response to starvation / cellular response to amino acid starvation / autophagy ...antibacterial innate immune response / lysosome localization / lysosome organization / humoral immune response / Transcriptional and post-translational regulation of MITF-M expression and activity / embryonic placenta development / positive regulation of autophagy / cellular response to starvation / cellular response to amino acid starvation / autophagy / sequence-specific double-stranded DNA binding / adaptive immune response / protein dimerization activity / 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 / lysosomal membrane / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor EB / MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
Similarity search - Domain/homology
Transcription factor EB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, G. / Li, P. / Lin, Y. / Liu, Z. / Sun, H. / Zhao, Z. / Fang, P. / Wang, J.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21778067 China
National Natural Science Foundation of China (NSFC)21977108 China
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: A small-molecule drug inhibits autophagy gene expression through the central regulator TFEB.
Authors: Lin, Y. / Shi, Q. / Yang, G. / Shi, F. / Zhou, Y. / Wang, T. / Xu, P. / Li, P. / Liu, Z. / Sun, H. / Zhao, Z. / Ding, K. / Wang, Z. / Feng, H. / Yu, B. / Fang, P. / Wang, J.
History
DepositionJun 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor EB
B: Transcription factor EB


Theoretical massNumber of molelcules
Total (without water)17,9332
Polymers17,9332
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-36 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.600, 54.600, 185.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcription factor EB / Class E basic helix-loop-helix protein 35 (bHLHe35)


Mass: 8966.413 Da / Num. of mol.: 2 / Fragment: HLHLZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFEB / Production host: Escherichia coli (E. coli) / References: UniProt: P19484
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Ethylene glycols, Buffer system 3, and Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→47.28 Å / Num. obs: 22446 / % possible obs: 99.2 % / Redundancy: 18.6 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.014 / Rrim(I) all: 0.058 / Net I/σ(I): 27.2 / Num. measured all: 417639 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0519.71.5333215116280.9180.3521.5732.1100
8.95-47.2814.20.024458532210.0060.0256899.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D8S

7d8s


Resolution: 2→47.28 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 1131 5.08 %
Rwork0.2215 21149 -
obs0.2223 22280 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.03 Å2 / Biso mean: 31.5986 Å2 / Biso min: 9.43 Å2
Refinement stepCycle: final / Resolution: 2→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 171 35 1400
Biso mean--42.13 50.84 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.090.27521390.272726282767100
2.09-2.20.29921170.233626382755100
2.2-2.340.25951510.31012317246890
2.34-2.520.2551340.233726442778100
2.52-2.770.21161450.220826682813100
2.77-3.170.28471680.216426602828100
3.18-40.20761030.199827372840100
4-47.280.20671740.199328573031100
Refinement TLS params.Method: refined / Origin x: -12.3803 Å / Origin y: 23.5608 Å / Origin z: 72.9923 Å
111213212223313233
T0.1527 Å20.0511 Å2-0.0175 Å2-0.2738 Å2-0.0368 Å2--0.1667 Å2
L1.7286 °2-1.2321 °2-2.746 °2-0.7438 °21.6316 °2--2.8634 °2
S-0.0625 Å °-0.266 Å °0.0338 Å °0.0707 Å °0.1366 Å °0.0045 Å °0.0621 Å °0.231 Å °-0.0671 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA248 - 321
2X-RAY DIFFRACTION1allB248 - 321
3X-RAY DIFFRACTION1allS1 - 254

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