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- PDB-7fdl: Crystal structure of transcription factor WER in complex with EGL3 -

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Basic information

Entry
Database: PDB / ID: 7fdl
TitleCrystal structure of transcription factor WER in complex with EGL3
Components
  • Transcription factor EGL1
  • Transcription factor WER
KeywordsTRANSCRIPTION / Transcription factor complex
Function / homology
Function and homology information


root hair cell differentiation / trichome differentiation / jasmonic acid mediated signaling pathway / epidermal cell fate specification / cell fate commitment / cell differentiation / transcription cis-regulatory region binding / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...root hair cell differentiation / trichome differentiation / jasmonic acid mediated signaling pathway / epidermal cell fate specification / cell fate commitment / cell differentiation / transcription cis-regulatory region binding / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
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 ...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 EGL1 / Transcription factor WER
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.897 Å
AuthorsLuo, Q. / Wang, B.
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 EGL1
B: Transcription factor WER
C: Transcription factor EGL1
D: Transcription factor WER
E: Transcription factor EGL1
F: Transcription factor WER
G: Transcription factor EGL1
H: Transcription factor WER
I: Transcription factor EGL1
J: Transcription factor WER
K: Transcription factor EGL1
L: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)168,73112
Polymers168,73112
Non-polymers00
Water0
1
K: Transcription factor EGL1
L: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcription factor EGL1
B: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area10880 Å2
MethodPISA
3
C: Transcription factor EGL1
D: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-8 kcal/mol
Surface area10700 Å2
MethodPISA
4
E: Transcription factor EGL1
F: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-9 kcal/mol
Surface area8800 Å2
MethodPISA
5
G: Transcription factor EGL1
H: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-7 kcal/mol
Surface area9720 Å2
MethodPISA
6
I: Transcription factor EGL1
J: Transcription factor WER


Theoretical massNumber of molelcules
Total (without water)28,1222
Polymers28,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-8 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.913, 193.392, 224.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and ((resid 75 and (name N or name...
21(chain D and ((resid 75 and (name N or name...
31(chain F and (resseq 75 or (resid 76 and (name...
41(chain H and ((resid 75 and (name N or name...
51(chain J and ((resid 75 and (name N or name...
12(chain A and (resseq 12:14 or (resid 16 and (name...
22(chain C and ((resid 12 and (name N or name...
32(chain G and (resseq 12:14 or resseq 16:51 or (resid...
42(chain I and ((resid 12 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRTHRTHR(chain B and ((resid 75 and (name N or name...BB759
121ASNASNSERSER(chain B and ((resid 75 and (name N or name...BB73 - 1177 - 51
131ASNASNSERSER(chain B and ((resid 75 and (name N or name...BB73 - 1177 - 51
141ASNASNSERSER(chain B and ((resid 75 and (name N or name...BB73 - 1177 - 51
151ASNASNSERSER(chain B and ((resid 75 and (name N or name...BB73 - 1177 - 51
211THRTHRTHRTHR(chain D and ((resid 75 and (name N or name...DD759
221GLYGLYSERSER(chain D and ((resid 75 and (name N or name...DD72 - 1176 - 51
231GLYGLYSERSER(chain D and ((resid 75 and (name N or name...DD72 - 1176 - 51
241GLYGLYSERSER(chain D and ((resid 75 and (name N or name...DD72 - 1176 - 51
251GLYGLYSERSER(chain D and ((resid 75 and (name N or name...DD72 - 1176 - 51
311THRTHRTHRTHR(chain F and (resseq 75 or (resid 76 and (name...FF759
321GLUGLUGLUGLU(chain F and (resseq 75 or (resid 76 and (name...FF7610
331PHEPHEASNASN(chain F and (resseq 75 or (resid 76 and (name...FF74 - 1138 - 47
411THRTHRTHRTHR(chain H and ((resid 75 and (name N or name...HH759
421ASNASNSERSER(chain H and ((resid 75 and (name N or name...HH73 - 1177 - 51
431ASNASNSERSER(chain H and ((resid 75 and (name N or name...HH73 - 1177 - 51
441ASNASNSERSER(chain H and ((resid 75 and (name N or name...HH73 - 1177 - 51
451ASNASNSERSER(chain H and ((resid 75 and (name N or name...HH73 - 1177 - 51
511THRTHRTHRTHR(chain J and ((resid 75 and (name N or name...JJ759
521PHEPHELEULEU(chain J and ((resid 75 and (name N or name...JJ74 - 1168 - 50
531PHEPHELEULEU(chain J and ((resid 75 and (name N or name...JJ74 - 1168 - 50
541PHEPHELEULEU(chain J and ((resid 75 and (name N or name...JJ74 - 1168 - 50
551PHEPHELEULEU(chain J and ((resid 75 and (name N or name...JJ74 - 1168 - 50
112ASNASNLYSLYS(chain A and (resseq 12:14 or (resid 16 and (name...AA12 - 145 - 7
122GLNGLNGLNGLN(chain A and (resseq 12:14 or (resid 16 and (name...AA169
132VALVALGLUGLU(chain A and (resseq 12:14 or (resid 16 and (name...AA9 - 2042 - 197
142VALVALGLUGLU(chain A and (resseq 12:14 or (resid 16 and (name...AA9 - 2042 - 197
212ASNASNASNASN(chain C and ((resid 12 and (name N or name...CC125
222ASNASNALAALA(chain C and ((resid 12 and (name N or name...CC12 - 2055 - 198
232ASNASNALAALA(chain C and ((resid 12 and (name N or name...CC12 - 2055 - 198
242ASNASNALAALA(chain C and ((resid 12 and (name N or name...CC12 - 2055 - 198
252ASNASNALAALA(chain C and ((resid 12 and (name N or name...CC12 - 2055 - 198
312ASNASNLYSLYS(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG12 - 145 - 7
322GLNGLNGLYGLY(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG16 - 519 - 44
332ILEILEILEILE(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG5346
342ASNASNGLUGLU(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG12 - 2045 - 197
352ASNASNGLUGLU(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG12 - 2045 - 197
362ASNASNGLUGLU(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG12 - 2045 - 197
372ASNASNGLUGLU(chain G and (resseq 12:14 or resseq 16:51 or (resid...GG12 - 2045 - 197
412ASNASNASNASN(chain I and ((resid 12 and (name N or name...II125
422ASPASPGLUGLU(chain I and ((resid 12 and (name N or name...II11 - 2044 - 197
432ASPASPGLUGLU(chain I and ((resid 12 and (name N or name...II11 - 2044 - 197
442ASPASPGLUGLU(chain I and ((resid 12 and (name N or name...II11 - 2044 - 197
452ASPASPGLUGLU(chain I and ((resid 12 and (name N or name...II11 - 2044 - 197

NCS ensembles :
ID
1
2

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Components

#1: Protein
Transcription factor EGL1 / Basic helix-loop-helix protein 2 / AtMYC146 / AtbHLH2 / bHLH 2 / Protein ENHANCER OF GLABRA 3 / ...Basic helix-loop-helix protein 2 / AtMYC146 / AtbHLH2 / bHLH 2 / Protein ENHANCER OF GLABRA 3 / Transcription factor EN 30 / bHLH transcription factor bHLH002


Mass: 21682.367 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BHLH2, EGL1, EGL3, EN30, MYC146, At1g63650, F24D7.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CAD0
#2: Protein
Transcription factor WER / Myb-related protein 66 / AtMYB66 / Protein WEREWOLF


Mass: 6439.416 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WER, MYB66, At5g14750, T9L3.50 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SEI0

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 200 mM magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.897→30 Å / Num. obs: 37043 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.052 / Rrim(I) all: 0.157 / Χ2: 0.96 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-36.10.70835850.1140.2920.770.7798.4
3-3.126.50.68336540.1720.2770.740.77999.5
3.12-3.277.20.61736570.4670.2370.6640.87199.7
3.27-3.447.50.5236810.7020.1950.5570.92299.7
3.44-3.657.50.40636600.8840.1530.4350.98799.9
3.65-3.938.70.28237000.9670.0980.2991.06299.9
3.93-4.339.70.19437040.9880.0630.2051.13999.8
4.33-4.95100.13237270.9940.0420.1391.125100
4.95-6.239.60.11237630.9950.0370.1180.99699.9
6.23-3010.40.05339120.9990.0170.0560.79999.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC7.0.076refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RRU

4rru


Resolution: 2.897→29.907 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2985 1578 4.99 %
Rwork0.2542 --
obs0.2565 31615 84.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.11 Å2 / Biso mean: 70 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.897→29.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8866 0 0 0 8866
Num. residues----1171
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B681X-RAY DIFFRACTION14.715TORSIONAL
12D681X-RAY DIFFRACTION14.715TORSIONAL
13F681X-RAY DIFFRACTION14.715TORSIONAL
14H681X-RAY DIFFRACTION14.715TORSIONAL
15J681X-RAY DIFFRACTION14.715TORSIONAL
21A2538X-RAY DIFFRACTION14.715TORSIONAL
22C2538X-RAY DIFFRACTION14.715TORSIONAL
23G2538X-RAY DIFFRACTION14.715TORSIONAL
24I2538X-RAY DIFFRACTION14.715TORSIONAL
LS refinement shellResolution: 2.8971→2.9905 Å
RfactorNum. reflection
Rfree0.3337 57
Rwork0.3096 -
obs-920
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)
12.6979-1.2580.10571.5750.02221.3277-0.2122-0.47920.11230.02130.2587-0.4501-0.09170.0509-0.02110.2710.04810.08560.6107-0.00980.4677-15.7922-42.338475.7255
21.5594-0.75930.03482.157-0.24361.22160.05930.3497-0.6341-0.3847-0.39080.1280.3543-0.03540.09730.65140.05740.10260.698-0.10620.5735-9.3344-62.447967.8307
32.3081-0.3293-0.63512.06050.25552.3516-0.06080.0874-0.0456-0.03090.09330.33960.0211-0.3526-0.03360.26490.0170.02490.3220.01170.2652-49.072-31.665370.3149
42.76250.0203-0.02153.80220.75973.4566-0.3071-0.03411.0857-0.48990.04780.7336-0.9948-0.32490.18060.7290.1478-0.07950.61310.06590.7253-52.8828-10.418862.5006
51.6485-0.0027-0.48962.5088-0.20582.0415-0.0727-0.2973-0.5533-0.5181-0.4534-0.07910.0245-0.19490.58581.0399-0.2195-0.24420.9180.11121.2474-68.9649.16575.288
60.1279-0.0372-0.19981.2452-0.60390.66570.06280.5780.0456-0.11060.20370.59280.0056-0.3966-0.09951.1789-0.4816-0.28251.20090.30282.3001-68.2293-12.268778.4606
71.8221-0.1401-0.16193.9376-1.00122.3109-0.11850.21430.0846-1.4860.0374-0.03090.98110.02660.07830.98310.01510.03180.47570.09030.5912-36.039112.020982.5019
82.8503-1.84660.75913.36771.11351.6454-0.3302-0.04040.510.28510.36080.3158-0.24190.3047-0.00170.7784-0.0586-0.07750.60980.01540.7559-39.394633.040588.8431
92.11660.33310.8721.89240.02732.01950.1017-0.51860.21840.6938-0.08990.1390.21430.0221-0.00230.68690.060.11520.4364-0.08070.3816-42.6074-14.912102.6612
100.3002-0.1236-0.22761.54990.36772.1955-0.0467-0.5061-0.55430.1969-0.4144-0.15110.9160.65560.13961.1670.3763-0.18490.87460.02470.6841-28.0662-31.3353106.3542
111.19991.031-0.74691.4126-0.31670.66830.3024-0.542-0.83390.85390.67720.95520.1006-0.64220.59470.41170.40650.52542.09091.011.1804-33.1834-62.729198.3302
121.6343-1.59191.10283.2783-0.93370.87090.0719-0.6822-0.60080.23970.39261.06250.0142-0.4581-0.40030.86020.56040.24851.99590.78881.5475-48.7504-52.512597.3569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 9:204 )A9 - 204
2X-RAY DIFFRACTION2(chain B and resseq 73:117)B73 - 117
3X-RAY DIFFRACTION3(chain C and resseq 12:205)C12 - 205
4X-RAY DIFFRACTION4(chain D and resseq 72:117)D72 - 117
5X-RAY DIFFRACTION5(chain E and resseq 16:119)E16 - 119
6X-RAY DIFFRACTION6(chain F and resseq 74:113)F74 - 113
7X-RAY DIFFRACTION7(chain G and resseq 12:204)G12 - 204
8X-RAY DIFFRACTION8(chain H and resseq 73:117)H73 - 117
9X-RAY DIFFRACTION9(chain I and resseq 11:204)I11 - 204
10X-RAY DIFFRACTION10(chain J and resseq 74:116)J74 - 116
11X-RAY DIFFRACTION11(chain K and resseq 13:202)K13 - 202
12X-RAY DIFFRACTION12(chain L and resseq 75:88)L75 - 88

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