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- PDB-7fdm: Crystal structure of transcription factor MYB29 in complex with MYC3 -

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Basic information

Entry
Database: PDB / ID: 7fdm
TitleCrystal structure of transcription factor MYB29 in complex with MYC3
Components
  • Transcription factor MYB29
  • Transcription factor MYC3
KeywordsTRANSCRIPTION / Transcription factor complex
Function / homology
Function and homology information


drought recovery / regulation of glucosinolate biosynthetic process / regulation of RNA binding transcription factor activity / regulation of response to water deprivation / cellular response to sulfur starvation / negative regulation of ethylene-activated signaling pathway / induced systemic resistance / mitochondria-nucleus signaling pathway / extracellular ATP signaling / response to insect ...drought recovery / regulation of glucosinolate biosynthetic process / regulation of RNA binding transcription factor activity / regulation of response to water deprivation / cellular response to sulfur starvation / negative regulation of ethylene-activated signaling pathway / induced systemic resistance / mitochondria-nucleus signaling pathway / extracellular ATP signaling / response to insect / anthocyanin-containing compound biosynthetic process / stomatal complex development / jasmonic acid mediated signaling pathway / response to high light intensity / response to jasmonic acid / bHLH transcription factor binding / response to water deprivation / defense response to fungus / hormone-mediated signaling pathway / response to bacterium / defense response / response to wounding / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Transcription factor AIB/MYC-like / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Helix-loop-helix DNA-binding domain superfamily ...Transcription factor AIB/MYC-like / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb 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. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Transcription factor MYC3 / Transcription factor MYB29
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, Q. / Wang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC31930017 China
CitationJournal: Nat.Plants / Year: 2021
Title: Structural insights into partner selection for MYB and bHLH transcription factor complexes.
Authors: Wang, B. / Luo, Q. / Li, Y. / Du, K. / Wu, Z. / Li, T. / Shen, W.H. / Huang, C.H. / Gan, J. / Dong, A.
History
DepositionJul 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor MYC3
B: Transcription factor MYC3
C: Transcription factor MYB29
D: Transcription factor MYB29


Theoretical massNumber of molelcules
Total (without water)53,3154
Polymers53,3154
Non-polymers00
Water25214
1
A: Transcription factor MYC3
C: Transcription factor MYB29


Theoretical massNumber of molelcules
Total (without water)26,6582
Polymers26,6582
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area9530 Å2
MethodPISA
2
B: Transcription factor MYC3
D: Transcription factor MYB29


Theoretical massNumber of molelcules
Total (without water)26,6582
Polymers26,6582
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.247, 85.247, 57.017
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 46 through 78 or resid 84...
21(chain B and (resid 46 through 53 or (resid 54...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASP(chain A and (resid 46 through 78 or resid 84...AA46 - 783 - 35
12GLYGLYGLYGLY(chain A and (resid 46 through 78 or resid 84...AA8441
13ASPASPASNASN(chain A and (resid 46 through 78 or resid 84...AA85 - 8642 - 43
14GLNGLNASNASN(chain A and (resid 46 through 78 or resid 84...AA46 - 2383 - 195
15GLNGLNASNASN(chain A and (resid 46 through 78 or resid 84...AA46 - 2383 - 195
16GLNGLNASNASN(chain A and (resid 46 through 78 or resid 84...AA46 - 2383 - 195
17GLNGLNASNASN(chain A and (resid 46 through 78 or resid 84...AA46 - 2383 - 195
21GLNGLNGLNGLN(chain B and (resid 46 through 53 or (resid 54...BB46 - 533 - 10
22GLNGLNGLNGLN(chain B and (resid 46 through 53 or (resid 54...BB5411
23GLNGLNASNASN(chain B and (resid 46 through 53 or (resid 54...BB46 - 2383 - 195
24GLNGLNASNASN(chain B and (resid 46 through 53 or (resid 54...BB46 - 2383 - 195
25GLNGLNASNASN(chain B and (resid 46 through 53 or (resid 54...BB46 - 2383 - 195
26GLNGLNASNASN(chain B and (resid 46 through 53 or (resid 54...BB46 - 2383 - 195

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Components

#1: Protein Transcription factor MYC3 / Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein ALTERED TRYPTOPHAN REGULATION 2 / ...Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein ALTERED TRYPTOPHAN REGULATION 2 / Transcription factor ATR2 / Transcription factor EN 36 / bHLH transcription factor bHLH005


Mass: 21587.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC3, ATR2, BHLH5, EN36, At5g46760, MZA15.18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FIP9
#2: Protein/peptide Transcription factor MYB29 / Myb-related protein 29 / AtMYB29 / Protein HIGH ALIPHATIC GLUCOSINOLATE 3 / Protein PRODUCTION OF ...Myb-related protein 29 / AtMYB29 / Protein HIGH ALIPHATIC GLUCOSINOLATE 3 / Protein PRODUCTION OF METHIONINE-DERIVED GLUCOSINOLATE 2


Mass: 5069.925 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYB29, HAG3, PMG2, At5g07690, MBK20.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FLR1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 20% (w/v) PEG 6000, 0.2 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15757 / % possible obs: 97.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 36.09 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.015 / Rrim(I) all: 0.043 / Χ2: 0.922 / Net I/σ(I): 11.6 / Num. measured all: 98697
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.30.42114890.1140.2440.4910.65391.3
2.59-2.693.50.40115210.2310.2270.4650.65994.9
2.69-2.823.70.36815390.4420.2010.4230.79396.2
2.82-2.964.20.29915550.7950.1460.3350.85795.8
2.96-3.155.50.22315960.9440.0950.2440.93798.3
3.15-3.396.70.14416080.9850.0560.1561.0599.3
3.39-3.7380.07616020.9980.0270.0811.13199.8
3.73-4.277.80.04916200.9980.0180.0521.12899.4
4.27-5.389.70.03316100.9990.0110.0350.94999.8
5.38-309.70.02616170.9990.0090.0280.67799.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RRU

4rru


Resolution: 2.5→27.9 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2.19 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 572 9.81 %
Rwork0.2321 11357 -
obs0.2355 12592 78.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.77 Å2 / Biso mean: 58.9161 Å2 / Biso min: 7.54 Å2
Refinement stepCycle: final / Resolution: 2.5→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 0 14 2870
Biso mean---31.49 -
Num. residues----372
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A990X-RAY DIFFRACTION4.088TORSIONAL
12B990X-RAY DIFFRACTION4.088TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60.3095290.304225428316
2.6-2.720.3116770.321170678344
2.72-2.860.34181080.30341044115265
2.86-3.040.3141500.29651402155287
3.04-3.280.3111720.27081582175498
3.28-3.610.26651710.23861578174999
3.61-4.120.22541630.22131592175599
4.13-5.190.25931890.188515991788100
5.2-27.90.24581760.20416001776100
Refinement TLS params.Method: refined / Origin x: 12.3177 Å / Origin y: 27.5724 Å / Origin z: -2.4515 Å
111213212223313233
T0.3437 Å20.1165 Å20.0576 Å2-0.1375 Å2-0.0013 Å2--0.2547 Å2
L2.6421 °2-0.4258 °2-0.9366 °2-2.7704 °2-0.5536 °2--3.2457 °2
S-0.2429 Å °0.3473 Å °-0.7212 Å °0.2956 Å °-0.6312 Å °-0.441 Å °1.3236 Å °0.7905 Å °-0.1224 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA46 - 238
2X-RAY DIFFRACTION1allB46 - 238
3X-RAY DIFFRACTION1allC184 - 203
4X-RAY DIFFRACTION1allD184 - 198
5X-RAY DIFFRACTION1allE2 - 16

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