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- PDB-5gnj: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 5gnj
TitleStructure of a transcription factor and DNA complex
Components
  • DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')
  • Transcription factor MYC2
KeywordsDNA BINDING PROTEIN/DNA / Transcription factor / DNA / complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / regulation of defense response to insect / regulation of secondary cell wall biogenesis / indole glucosinolate biosynthetic process / response to desiccation / positive regulation of flavonoid biosynthetic process / extracellular ATP signaling / stomatal complex development / : / response to jasmonic acid ...: / regulation of defense response to insect / regulation of secondary cell wall biogenesis / indole glucosinolate biosynthetic process / response to desiccation / positive regulation of flavonoid biosynthetic process / extracellular ATP signaling / stomatal complex development / : / response to jasmonic acid / : / response to abscisic acid / abscisic acid-activated signaling pathway / response to wounding / kinase binding / sequence-specific DNA binding / protein homotetramerization / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / 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 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor MYC2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLian, T. / Xu, Y. / Su, X.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Cell Rep / Year: 2017
Title: Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA.
Authors: Lian, T.F. / Xu, Y.P. / Li, L.F. / Su, X.D.
History
DepositionJul 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
G: Transcription factor MYC2
I: Transcription factor MYC2
K: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
L: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')
A: Transcription factor MYC2
B: Transcription factor MYC2
C: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
D: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')
E: Transcription factor MYC2
F: Transcription factor MYC2
H: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
J: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')
M: Transcription factor MYC2
N: Transcription factor MYC2
O: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
P: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)120,21616
Polymers120,21616
Non-polymers00
Water1,11762
1
G: Transcription factor MYC2
I: Transcription factor MYC2
K: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
L: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers30,0544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-67 kcal/mol
Surface area13520 Å2
MethodPISA
2
A: Transcription factor MYC2
B: Transcription factor MYC2
C: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
D: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers30,0544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-64 kcal/mol
Surface area13880 Å2
MethodPISA
3
E: Transcription factor MYC2
F: Transcription factor MYC2
H: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
J: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers30,0544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-62 kcal/mol
Surface area13300 Å2
MethodPISA
4
M: Transcription factor MYC2
N: Transcription factor MYC2
O: DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')
P: DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers30,0544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-60 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 79.700, 102.800
Angle α, β, γ (deg.)90.000, 105.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A
21chain B
31chain E
41chain F
51chain G
61chain I
71chain M
81chain N
12chain C
22chain H
32chain K
42chain O
13chain D
23chain J
33chain L
43chain P

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNARGARGchain AAE452 - 5258 - 81
21GLUGLUARGARGchain BBF449 - 5255 - 81
31ASNASNARGARGchain EEI452 - 5258 - 81
41ASNASNGLYGLYchain FFJ452 - 5248 - 80
51ASNASNGLYGLYchain GGA452 - 5248 - 80
61GLUGLUALAALAchain IIB449 - 5235 - 79
71ASNASNGLYGLYchain MMM452 - 5248 - 80
81ASNASNGLYGLYchain NNN452 - 5248 - 80
12DADADCDCchain CCG603 - 6161 - 14
22DADADCDCchain HHK603 - 6161 - 14
32DADADCDCchain KKC603 - 6161 - 14
42DGDGDCDCchain OOO604 - 6162 - 14
13DGDGDCDCchain DDH804 - 8172 - 15
23DGDGDCDCchain JJL805 - 8173 - 15
33DGDGDCDCchain LLD804 - 8172 - 15
43DGDGDCDCchain PPP805 - 8163 - 14

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Transcription factor MYC2 / AtMYC2 / Basic helix-loop-helix protein 6 / bHLH 6 / Protein JASMONATE INSENSITIVE 1 / R-homologous ...AtMYC2 / Basic helix-loop-helix protein 6 / bHLH 6 / Protein JASMONATE INSENSITIVE 1 / R-homologous Arabidopsis protein 1 / RAP-1 / Transcription factor EN 38 / Z-box binding factor 1 protein / bHLH transcription factor bHLH006 / rd22BP1


Mass: 10436.967 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 446-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MYC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q39204
#2: DNA chain
DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)-3')


Mass: 4588.001 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)-3')


Mass: 4591.969 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.66→49.65 Å / Num. obs: 32765 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 63.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.02
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.66-2.70.5631.510.629161.5
2.7-2.80.5831.910.618194.3
2.8-30.3892.730.795198.2
3-40.07810.890.992196.1
4-60.03225.160.997195.1
6-80.02827.390.998193.5
8-100.02333.060.998192.8
10-200.02132.830.998188.1
20-300.02131.40.998164.4
300.03115.73115.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.649 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.7
RfactorNum. reflection% reflection
Rfree0.2733 1612 5.06 %
Rwork0.2056 --
obs0.2091 31841 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 247.44 Å2 / Biso mean: 79.9792 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.7→49.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 2190 0 62 6894
Biso mean---58.39 -
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117115
X-RAY DIFFRACTIONf_angle_d1.43510023
X-RAY DIFFRACTIONf_chiral_restr0.0641163
X-RAY DIFFRACTIONf_plane_restr0.008912
X-RAY DIFFRACTIONf_dihedral_angle_d23.7132868
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2801X-RAY DIFFRACTION15.081TORSIONAL
12B2801X-RAY DIFFRACTION15.081TORSIONAL
13E2801X-RAY DIFFRACTION15.081TORSIONAL
14F2801X-RAY DIFFRACTION15.081TORSIONAL
15G2801X-RAY DIFFRACTION15.081TORSIONAL
16I2801X-RAY DIFFRACTION15.081TORSIONAL
17M2801X-RAY DIFFRACTION15.081TORSIONAL
18N2801X-RAY DIFFRACTION15.081TORSIONAL
21C532X-RAY DIFFRACTION15.081TORSIONAL
22H532X-RAY DIFFRACTION15.081TORSIONAL
23K532X-RAY DIFFRACTION15.081TORSIONAL
24O532X-RAY DIFFRACTION15.081TORSIONAL
31D514X-RAY DIFFRACTION15.081TORSIONAL
32J514X-RAY DIFFRACTION15.081TORSIONAL
33L514X-RAY DIFFRACTION15.081TORSIONAL
34P514X-RAY DIFFRACTION15.081TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.77950.42281400.35592448258893
2.7795-2.86920.34911410.30982559270098
2.8692-2.97170.34761150.26872569268498
2.9717-3.09070.35311350.26482599273498
3.0907-3.23130.31881310.25962543267498
3.2313-3.40160.28131290.20552549267897
3.4016-3.61470.29251290.20282513264295
3.6147-3.89370.26061280.19792482261095
3.8937-4.28530.21451330.1792488262194
4.2853-4.90490.2361460.16782516266296
4.9049-6.17780.26591460.1952506265295
6.1778-49.6570.26811390.18752457259691
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)
16.11881.2544-1.53572.8923-3.11893.44490.18830.0451-0.0583-0.29840.1485-0.07360.3149-0.659-0.54490.4905-0.1246-0.03180.39450.04290.485516.894-27.89665.732
25.41153.0547-1.55052.7070.48952.13460.73480.65260.28672.982-0.37581.4988-0.593-0.058-0.27150.86220.07880.11990.447-0.01180.98711.462518.996725.5593
36.24921.6940.04447.95661.02453.7922-0.33670.6075-0.15460.0438-0.2963-1.34430.67511.15170.59020.51450.09510.0090.65110.13790.63722.07982.59511.9151
46.131-0.7025-0.67823.9091-1.93167.63050.3771.5663-0.0475-0.4695-0.6033-0.06850.6425-0.01090.2770.566-0.1639-0.12490.5494-0.14910.463518.40554.846715.0865
55.61460.53130.80475.43320.0894.9174-0.10050.19790.3536-0.4830.1165-0.3285-0.21420.40430.03890.4832-0.160.10120.4374-0.09320.48633.459-10.73665.819
63.57871.9740.87332.53652.35362.9036-0.10451.25420.15862.2693-0.3251.52710.41020.49090.29530.6039-0.02-0.02390.501-0.00190.629439.341-58.14325.5108
76.0668-0.9278-0.26897.36042.83274.083-0.88551.1921-0.0639-0.4966-0.45181.0047-2.0904-1.25451.11640.9098-0.0584-0.16010.9232-0.21970.900128.9729-41.989712.1144
88.08431.26230.21784.92111.4123.49880.16781.6212-0.44910.0472-0.4780.8327-0.58070.39080.28230.6928-0.1232-0.01530.77450.04720.196832.7101-43.900714.8807
93.7589-0.90373.18932.90212.51248.3422-0.26581.05260.4234-0.32540.2073-0.0223-1.22581.12610.11430.562-0.2847-0.06820.66930.10420.564350.712-14.74965.233
103.4425-2.73561.12852.69580.03353.17490.69111.6711-1.454-1.3639-1.50071.2752.27280.84230.7121.46260.04490.03850.8775-0.09641.002459.3299-42.700512.4285
117.4328-0.72192.21852.52951.71539.9727-0.99150.22152.1144-0.1331-0.2891.1792-2.5326-0.42621.28861.11940.2704-0.30521.1734-0.04881.21947.3744-25.74430.9317
125.5816-1.9032-3.20228.35320.8792.78690.05941.13170.974-0.3851-1.12130.5618-1.84650.5251.14221.3004-0.0925-0.1970.75060.13390.806749.4194-26.29346.0116
133.812-3.70954.18238.8786-5.62765.1027-0.08530.4371-1.5292.50610.28-0.26531.62435.5067-0.48151.34970.55040.08561.75970.22810.965864.9833-42.85368.9656
144.6420.3552-0.96345.00970.89222.7162-0.57890.7953-0.3503-0.61220.30050.40560.55770.97990.26760.8799-0.4213-0.0010.86330.04750.4865-0.576-23.86764.707
157.53893.2181-1.36554.3612.98795.58350.35411.87460.6265-0.2049-0.19450.1009-0.90610.0581-0.19771.2062-0.15410.04331.08140.32930.616-0.8622-9.63386.2631
163.4418-1.0963.11295.32050.88163.5650.24561.638-0.9213-0.3165-0.62830.49911.66420.43270.33281.3358-0.21560.08281.0464-0.07031.0815.1487-18.11857.3624
175.68230.80442.84116.33750.91532.01120.66742.4328-0.28670.15920.12210.6683-2.1037-2.1506-0.35271.39530.1594-0.08281.95880.46160.891-9.8126-3.60423.7533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND RESID 505:524 )G505 - 524
2X-RAY DIFFRACTION2( CHAIN K AND RESID 603:607 )K603 - 607
3X-RAY DIFFRACTION3( CHAIN K AND RESID 608:616 )K608 - 616
4X-RAY DIFFRACTION4( CHAIN L AND RESID 804:817 )L804 - 817
5X-RAY DIFFRACTION5( CHAIN A AND RESID 505:525 )A505 - 525
6X-RAY DIFFRACTION6( CHAIN C AND RESID 603:607 )C603 - 607
7X-RAY DIFFRACTION7( CHAIN C AND RESID 608:616 )C608 - 616
8X-RAY DIFFRACTION8( CHAIN D AND RESID 804:817 )D804 - 817
9X-RAY DIFFRACTION9( CHAIN E AND RESID 505:525 )E505 - 525
10X-RAY DIFFRACTION10( CHAIN H AND RESID 603:610 )H603 - 610
11X-RAY DIFFRACTION11( CHAIN H AND RESID 611:616 )H611 - 616
12X-RAY DIFFRACTION12( CHAIN J AND RESID 805:812 )J805 - 812
13X-RAY DIFFRACTION13( CHAIN J AND RESID 813:817 )J813 - 817
14X-RAY DIFFRACTION14( CHAIN M AND RESID 505:524 )M505 - 524
15X-RAY DIFFRACTION15( CHAIN O AND RESID 604:616 )O604 - 616
16X-RAY DIFFRACTION16( CHAIN P AND RESID 805:811 )P805 - 811
17X-RAY DIFFRACTION17( CHAIN P AND RESID 812:816 )P812 - 816

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