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- PDB-7x5f: Nrf2-MafG heterodimer bound with CsMBE2 -

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Basic information

Entry
Database: PDB / ID: 7x5f
TitleNrf2-MafG heterodimer bound with CsMBE2
Components
  • (Synthetic DNA) x 2
  • Nuclear factor erythroid 2-related factor 2
  • Transcription factor MafG
KeywordsTRANSCRIPTION/DNA / Transcription factor / CNC-bZIP / Stress response / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / membraneless organelle / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response ...aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / membraneless organelle / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals / negative regulation of vascular associated smooth muscle cell migration / regulation of cellular response to oxidative stress / regulation of epidermal cell differentiation / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / positive regulation of ubiquitin-dependent protein catabolic process / mediator complex / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / cellular response to angiotensin / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of ferroptosis / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of cardiac muscle cell apoptotic process / proteasomal ubiquitin-independent protein catabolic process / regulation of innate immune response / adult behavior / regulation of embryonic development / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / negative regulation of endothelial cell apoptotic process / cellular response to glucose starvation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to copper ion / cell redox homeostasis / response to ischemia / transcription coregulator binding / protein-DNA complex / positive regulation of D-glucose import / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / molecular condensate scaffold activity / Heme signaling / positive regulation of neuron projection development / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / sequence-specific double-stranded DNA binding / KEAP1-NFE2L2 pathway / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / Neddylation / regulation of cell population proliferation / Factors involved in megakaryocyte development and platelet production / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / sequence-specific DNA binding / response to oxidative stress / Potential therapeutics for SARS / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transcription factor Maf family / : / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor MafG / Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSengoku, T. / Shiina, M. / Suzuki, K. / Hamada, K. / Sato, K. / Uchiyama, A. / Okada, C. / Baba, S. / Ohta, T. / Motohashi, H. ...Sengoku, T. / Shiina, M. / Suzuki, K. / Hamada, K. / Sato, K. / Uchiyama, A. / Okada, C. / Baba, S. / Ohta, T. / Motohashi, H. / Yamamoto, M. / Ogata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis of transcription regulation by CNC family transcription factor, Nrf2.
Authors: Sengoku, T. / Shiina, M. / Suzuki, K. / Hamada, K. / Sato, K. / Uchiyama, A. / Kobayashi, S. / Oguni, A. / Itaya, H. / Kasahara, K. / Moriwaki, H. / Watanabe, C. / Honma, T. / Okada, C. / ...Authors: Sengoku, T. / Shiina, M. / Suzuki, K. / Hamada, K. / Sato, K. / Uchiyama, A. / Kobayashi, S. / Oguni, A. / Itaya, H. / Kasahara, K. / Moriwaki, H. / Watanabe, C. / Honma, T. / Okada, C. / Baba, S. / Ohta, T. / Motohashi, H. / Yamamoto, M. / Ogata, K.
History
DepositionMar 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Transcription factor MafG
B: Nuclear factor erythroid 2-related factor 2
C: Synthetic DNA
D: Synthetic DNA
E: Transcription factor MafG
F: Nuclear factor erythroid 2-related factor 2
G: Synthetic DNA
H: Synthetic DNA


Theoretical massNumber of molelcules
Total (without water)70,2498
Polymers70,2498
Non-polymers00
Water1267
1
A: Transcription factor MafG
B: Nuclear factor erythroid 2-related factor 2
C: Synthetic DNA
D: Synthetic DNA


Theoretical massNumber of molelcules
Total (without water)35,1254
Polymers35,1254
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-50 kcal/mol
Surface area19040 Å2
MethodPISA
2
E: Transcription factor MafG
F: Nuclear factor erythroid 2-related factor 2
G: Synthetic DNA
H: Synthetic DNA


Theoretical massNumber of molelcules
Total (without water)35,1254
Polymers35,1254
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-52 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.171, 54.686, 85.952
Angle α, β, γ (deg.)90.000, 99.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Transcription factor MafG / V-maf musculoaponeurotic fibrosarcoma oncogene homolog G / hMAF


Mass: 12071.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAFG / Production host: Escherichia coli (E. coli) / References: UniProt: O15525
#2: Protein Nuclear factor erythroid 2-related factor 2 / NF-E2-related factor 2 / NFE2-related factor 2 / Nrf-2 / HEBP1 / Nuclear factor / erythroid derived 2 / like 2


Mass: 13255.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFE2L2, NRF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16236
#3: DNA chain Synthetic DNA


Mass: 4905.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Synthetic DNA


Mass: 4892.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 50 mM MES monohydrate (pH 5.6), 20 mM KCl, 10 mM MgSO4 heptahydrate, 7%(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45.27 Å / Num. obs: 34821 / % possible obs: 99.22 % / Redundancy: 7.3 % / Biso Wilson estimate: 65.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.18
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.7533 / Num. unique obs: 3266 / CC1/2: 0.81 / % possible all: 93.78

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A5T

3a5t


Resolution: 2.6→45.27 Å / SU ML: 0.3575 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 1747 5.02 %
Rwork0.2259 33074 -
obs0.2276 34821 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 1300 0 7 4557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554728
X-RAY DIFFRACTIONf_angle_d0.75386614
X-RAY DIFFRACTIONf_chiral_restr0.0377754
X-RAY DIFFRACTIONf_plane_restr0.0059638
X-RAY DIFFRACTIONf_dihedral_angle_d23.86761067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.40541160.32592601X-RAY DIFFRACTION93.53
2.68-2.760.38321300.33262743X-RAY DIFFRACTION99.38
2.76-2.860.39651360.34842748X-RAY DIFFRACTION99.69
2.86-2.980.43631520.37362730X-RAY DIFFRACTION99.79
2.98-3.110.31731400.28412738X-RAY DIFFRACTION99.97
3.11-3.280.27641640.23682743X-RAY DIFFRACTION99.05
3.28-3.480.27311630.22732733X-RAY DIFFRACTION99.62
3.48-3.750.28521340.24272771X-RAY DIFFRACTION99.93
3.75-4.130.231280.20282811X-RAY DIFFRACTION100
4.13-4.720.21071650.19052764X-RAY DIFFRACTION99.97
4.72-5.950.25751500.20762816X-RAY DIFFRACTION100
5.95-45.270.21511690.19152876X-RAY DIFFRACTION99.77
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)
17.5545142143-2.485449279296.820967400532.00234857765-3.348759616022.000605022940.795979114931.103367421381.13920953442-0.88785800352-1.02503533968-2.053575845983.844478275431.036278613190.234682725961.221243053180.1635889809110.1274558704881.402597385850.2678974146330.930601861972-17.1987698032-46.0597078176-18.8561861182
28.01349093497-0.0904933261879-4.066165564641.73480904065-1.948264743026.05557497290.05334807938651.514830812240.760450573253-0.553551302127-0.557668938342-2.20832192366-0.525481221791.896797823710.5561479178190.948778748726-0.294317317220.2100261734321.923370030070.3343667043751.5551117655-14.1607298147-34.2478341386-27.9230086461
35.57483804995-0.812922018231-1.307233853092.42082330993-0.318504421582.375234843690.131696786588-0.2294290939760.314545624728-0.2276177888-0.1553294865880.0470906057921-0.1576707053080.3774294350170.03607549636190.531926099376-0.0837653172451-0.05258021690060.3306519210330.04507799078140.408030811894-53.9650224634-30.1367190159-14.5444147224
40.868627175403-0.7696832173340.4549527406364.96289570621-3.311166873453.6842105468-0.0682162367479-0.69010604547-0.506420698238-0.85364811462-0.149537932154-0.0380567418210.6002646955530.7083910586740.2689312305040.8337116161030.1347148155690.2227360104230.8047160261070.4008530965240.703611227686-39.2300576222-53.242800286-13.4223233632
52.75459094828-1.292939968453.418026727555.12348720507-3.887201868589.01238508606-0.1882378997711.29559161283-0.022686456159-0.865109845571-0.07956903322470.105806305070.4823472795831.104980965380.3142770127521.528758195130.3872610362520.2532780864121.405760202410.3828010793220.690269639328-36.0542906226-42.6386628888-34.9619709754
68.240094728421.99994278252-2.29893951971.999923046731.412009774676.131055648120.214771898779-0.16833290682-0.184064801793-0.9435702278330.5810185652392.28890135672-0.723830882377-2.0185320087-0.8073486959131.542817909440.389713158625-0.0541393607531.630594987610.9055320689381.54447204972-37.8531039248-30.9021995024-38.708898459
73.033813491471.87360904023-5.100985027413.20647569796-0.8287590251572.001541230110.00443806150370.2747090009380.312466732738-0.286951175978-0.693155445644-0.6455360535950.5704048206562.717521122980.6123234718711.184520305730.2522263100670.2758095377491.619557808570.6565925640020.728869544926-30.9179724597-33.6726792514-33.451567371
88.9407374166-1.48667850311-0.04715359600094.39199138466-3.884402452069.62621575806-0.0780278545480.0340212819424-0.640008997932-0.239140371216-0.854160995411-0.9971411812161.369228417220.9531508059330.9488282238450.73489889211-0.00206640778230.09976764119840.5052772130930.1812567815190.700419126247-38.6479346977-51.1819537738-16.3775945753
94.20815596455-0.1310882191743.146834787815.274330145971.921447843084.215710702710.64925443831-1.302489361470.4594685604811.170850114540.2008545282790.0722551649428-0.4029281293281.04041278887-0.8673105559181.2305687902-0.257658468160.2764716282191.52369233315-0.2233707828250.901718211851-43.2895493075-10.623573827847.155050103
109.87866436379-3.45888569268-8.189727689352.236205957772.98733625626.869373151040.0967580135418-0.0393948348230.5866470239250.2651009966190.142300361032-0.4038030089130.120248273644-0.191247107493-0.227382619320.4888194850650.0182540898832-0.04003186253430.732628382733-0.01543354504390.491382550746-12.5333030034-26.422136821415.5492687516
112.002205791021.998133871593.436261758852.00157535788-7.252864911715.60234352147-0.625701726616-0.510067172092-0.1919495345680.7704701385090.642516621799-0.1537511147320.0307336206433-0.3765178265290.00306277555110.727435604498-0.0003280145525040.1506228841580.486210780282-0.04003276279160.548774369798-61.9311401934-22.421492230914.7285082349
128.907401198491.10625666544-3.678736178018.94912196231-0.1240127158917.12065396751-0.2078379401691.71297823181-1.20507006122-1.09421908027-0.08028119415470.1393808727410.680580530787-0.9127857296670.2713419512590.593959579453-0.08029999497050.0278880880510.616383410366-0.1078946787110.456926597792-58.8866671147-22.43395858664.38275680105
134.5960303313-2.80336408449-0.7066874059198.934041364220.7210001937612.89419881110.6575973825532.0830515319-0.397913238398-2.31772668347-0.5023542164690.3058755468110.008736757904820.00445926170454-0.1470184734410.885176564099-0.0545503604006-0.02985787028961.22766524345-0.04198977184280.455746244533-59.6653574373-16.3197545185-2.64759342631
149.27080786222-2.3489089913-0.167293911340.7659806477590.1487218472510.4618645252630.1151838837160.0378050430431-0.507061390535-0.0270771282131-0.101803058323-0.01623153896510.1195347669620.259011549609-0.00454765346160.4748077697390.04205740570170.08665583955470.6064389433970.06939253156420.466408601781-20.3969335076-28.85517002110.4554064834
154.044263359010.143650901293-1.893395299870.59664422935-0.07078479983623.100839566620.384831060824-0.3394191541170.1491637572440.442977722578-0.006372275062030.184743313301-0.4491661183140.571067792696-0.3738564276781.225087500660.1922125586470.531913067471.736089556671.147195460850.0327766202876-40.242022256-25.934753502939.4046835337
164.8654930394-0.426339633310.748829135737.93341297979-2.009749158614.75777401289-0.210488772316-0.2010816021440.3006975253970.178356890830.0379423329373-0.5488674919660.08477128773671.327489585590.2368848416470.7677448114210.04374639338270.0476415096410.7335732801630.1267500132830.402142970646-40.6287410389-16.367420731215.4546794954
176.15363895572-3.534936434976.185818215912.03013019146-3.552919009526.215415457690.790362423168-0.4376461305640.415564926759-0.398693336957-0.1809387589320.3558470052360.576847855367-0.0572928635211-0.577617158490.774332992749-0.03353439526480.1299425617510.895120234430.2916882792850.532885167473-42.4690195383-14.09767530893.21710866768
188.390773386040.02708986948691.94150674482.002988758144.227131573242.22882762785-0.117062004795-0.3248566329250.6620680628760.5661851438210.2126413011010.1289597174970.759954215639-0.4602946061-0.06735693933590.669765834175-0.06987666917220.03206076614320.6521308461190.05719860884950.415250982644-37.9654087511-15.22564796920.6979174445
192.344453494742.861373238351.1289728816.67315783225-2.327551561842.007638880630.379501173655-0.639190556569-0.8842543737010.343852550394-0.658807676510.00400503852991.765649244970.7555126854010.2124726573151.746774622990.2660215650320.2244002375351.135256942630.5114302978930.655493601001-44.2464912554-29.546872388732.5405751117
200.9971289042131.483801272040.6469927642752.234757887780.9136677049870.4998717389340.08210001494510.144506328383-1.422883342440.2300080413390.02707196522080.7350395668731.096858417760.10608546906-0.1219253815931.555337859340.07386303869150.2282325689650.730504720481-0.1672795091341.68695305825-43.1862653286-73.5960678656-21.7955150237
218.25974730879-4.92892652032-2.36936786214.768021471961.502983247151.540341898060.1173036404150.247783033264-0.0922872129521-0.253095354475-0.1440751479530.438163197272-0.0568764525947-0.07141201142170.01561358790430.429252370448-0.0606163766809-0.03220091752810.4512415383610.05640195522680.415429041062-64.2092233084-34.9712521004-14.59215658
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'F' and (resid 453 through 463 )FF453 - 4631 - 11
22chain 'F' and (resid 464 through 491 )FF464 - 49112 - 39
33chain 'F' and (resid 492 through 558 )FF492 - 55840 - 106
44chain 'G' and (resid 0 through 9 )GG0 - 9
55chain 'G' and (resid 10 through 14 )GG10 - 14
66chain 'G' and (resid 15 through 15 )GG15
77chain 'H' and (resid 0 through 4 )HH0 - 4
88chain 'H' and (resid 5 through 15 )HH5 - 15
99chain 'A' and (resid 23 through 45 )AA23 - 451 - 23
1010chain 'A' and (resid 46 through 122 )AA46 - 12224 - 100
1111chain 'B' and (resid 454 through 463 )BB454 - 4631 - 10
1212chain 'B' and (resid 464 through 477 )BB464 - 47711 - 24
1313chain 'B' and (resid 478 through 491 )BB478 - 49125 - 38
1414chain 'B' and (resid 492 through 558 )BB492 - 55839 - 105
1515chain 'C' and (resid 0 through 4 )CC0 - 4
1616chain 'C' and (resid 5 through 15 )CC5 - 15
1717chain 'D' and (resid 0 through 4 )DD0 - 4
1818chain 'D' and (resid 5 through 9 )DD5 - 9
1919chain 'D' and (resid 10 through 15 )DD10 - 15
2020chain 'E' and (resid 27 through 44 )EE27 - 441 - 18
2121chain 'E' and (resid 45 through 121 )EE45 - 12119 - 95

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