[English] 日本語
Yorodumi
- PDB-7d8r: MITF HLHLZ structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d8r
TitleMITF HLHLZ structure
ComponentsMicrophthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / regulation of RNA biosynthetic process / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / regulation of osteoclast differentiation ...melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / regulation of RNA biosynthetic process / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / Regulation of MITF-M-dependent genes involved in apoptosis / camera-type eye development / E-box binding / Regulation of MITF-M-dependent genes involved in pigmentation / SUMOylation of transcription factors / cell fate commitment / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / osteoclast differentiation / negative regulation of cell migration / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of cell population proliferation / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / tRNA binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / lysosomal membrane / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / : / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Helix-loop-helix DNA-binding domain ...MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / : / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Methionyl-tRNA synthetase beta subunit / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Aquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsGuo, M. / 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: Cell Res. / Year: 2023
Title: A unique hyperdynamic dimer interface permits small molecule perturbation of the melanoma oncoprotein MITF for melanoma therapy.
Authors: Liu, Z. / Chen, K. / Dai, J. / Xu, P. / Sun, W. / Liu, W. / Zhao, Z. / Bennett, S.P. / Li, P. / Ma, T. / Lin, Y. / Kawakami, A. / Yu, J. / Wang, F. / Wang, C. / Li, M. / Chase, P. / Hodder, ...Authors: Liu, Z. / Chen, K. / Dai, J. / Xu, P. / Sun, W. / Liu, W. / Zhao, Z. / Bennett, S.P. / Li, P. / Ma, T. / Lin, Y. / Kawakami, A. / Yu, J. / Wang, F. / Wang, C. / Li, M. / Chase, P. / Hodder, P. / Spicer, T.P. / Scampavia, L. / Cao, C. / Pan, L. / Dong, J. / Chen, Y. / Yu, B. / Guo, M. / Fang, P. / Fisher, D.E. / Wang, J.
History
DepositionOct 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 16, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _software.version / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sheet_id
Description: Real space R-factor / Details: refined some sidechain outliers / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
B: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
C: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
D: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Theoretical massNumber of molelcules
Total (without water)82,4044
Polymers82,4044
Non-polymers00
Water68538
1
A: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
B: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Theoretical massNumber of molelcules
Total (without water)41,2022
Polymers41,2022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-25 kcal/mol
Surface area21340 Å2
MethodPISA
2
C: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
D: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Theoretical massNumber of molelcules
Total (without water)41,2022
Polymers41,2022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-27 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.910, 78.120, 80.590
Angle α, β, γ (deg.)93.180, 105.030, 105.620
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Mass: 20600.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fusion protein of Microphthalmia-associated transcription factor and Methionyl-tRNA synthetase beta subunit
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aquifex aeolicus VF5 (bacteria)
Gene: MITF, BHLHE32, metG', aq_422 / Strain: VF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O75030, UniProt: O66738
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES, KCl, PO/OH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3→77.124 Å / Num. all: 18512 / Num. obs: 18512 / % possible obs: 98.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 101.16 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.061 / Rsym value: 0.052 / Net I/av σ(I): 6 / Net I/σ(I): 12.7 / Num. measured all: 72600
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3-3.163.90.5861.31042726510.3410.6780.5862.498
3.16-3.353.90.292.61011625760.1690.3350.294.498.2
3.35-3.593.90.1734.2945524080.1010.2010.1736.797.9
3.59-3.873.90.116.3878722410.0640.1270.119.898.5
3.87-4.243.90.0679.7822420870.0390.0770.06714.598.4
4.24-4.743.90.05111734018680.030.0590.05119.898.5
4.74-5.483.90.04712.6640216280.0270.0540.04721.898.6
5.48-6.713.90.04412.1549314020.0260.0510.04422.498.9
6.71-9.493.90.03813.6418010690.0220.0440.03827.299
9.49-38.6933.70.03714.621765820.0230.0430.03728.795.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→38.693 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 2.1 / Phase error: 44.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3182 946 5.12 %
Rwork0.2847 17538 -
obs0.2866 18484 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.3 Å2 / Biso mean: 117.6446 Å2 / Biso min: 45.18 Å2
Refinement stepCycle: final / Resolution: 3→38.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 0 38 4798
Biso mean---85.48 -
Num. residues----684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0001-3.15820.44461200.4415248198
3.1582-3.3560.40451460.3918250098
3.356-3.61490.43441410.3698249598
3.6149-3.97840.39931410.3486251098
3.9784-4.55330.30411390.2849253698
4.5533-5.73370.29831290.2587251999
5.7337-38.6930.26491300.2293249798
Refinement TLS params.Method: refined / Origin x: 6.3472 Å / Origin y: -1.5648 Å / Origin z: 0.1995 Å
111213212223313233
T0.4673 Å20.0322 Å20.0158 Å2-0.6515 Å2-0.0609 Å2--0.5208 Å2
L0.1721 °20.0593 °20.1306 °2-2.5592 °2-0.6172 °2---0.8018 °2
S0.4182 Å °0.0009 Å °0.0228 Å °-0.0087 Å °-0.3756 Å °0.1511 Å °0.0108 Å °-0.093 Å °-0.0405 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA326 - 502
2X-RAY DIFFRACTION1allB326 - 502
3X-RAY DIFFRACTION1allC326 - 502
4X-RAY DIFFRACTION1allD326 - 502
5X-RAY DIFFRACTION1allE1 - 39

+
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