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- PDB-6bz1: MEF2 Chimera D83V mutant/DNA complex -

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Basic information

Entry
Database: PDB / ID: 6bz1
TitleMEF2 Chimera D83V mutant/DNA complex
Components
  • DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
  • DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
  • MEF2 CHIMERA
KeywordsTRANSCRIPTION/DNA / MEF2 / Transcription Factor / D83V mutant / conformation switch / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / cardiac conduction / mitochondrial genome maintenance / dendrite morphogenesis / muscle organ development / histone acetyltransferase binding / Myogenesis / positive regulation of cardiac muscle hypertrophy ...ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / cardiac conduction / mitochondrial genome maintenance / dendrite morphogenesis / muscle organ development / histone acetyltransferase binding / Myogenesis / positive regulation of cardiac muscle hypertrophy / SMAD binding / ERK/MAPK targets / cellular response to calcium ion / positive regulation of glucose import / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding / MAPK cascade / sequence-specific double-stranded DNA binding / cell junction / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / apoptotic process / chromatin binding / chromatin / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / SRF-like / Transcription factor, MADS-box / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. ...Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / SRF-like / Transcription factor, MADS-box / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte-specific enhancer factor 2A / Myocyte-specific enhancer factor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsLei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: The Cancer Mutation D83V Induces an alpha-Helix to beta-Strand Conformation Switch in MEF2B.
Authors: Lei, X. / Kou, Y. / Fu, Y. / Rajashekar, N. / Shi, H. / Wu, F. / Xu, J. / Luo, Y. / Chen, L.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 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
C: MEF2 CHIMERA
D: MEF2 CHIMERA
G: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
H: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
A: MEF2 CHIMERA
B: MEF2 CHIMERA
E: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
F: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)63,0298
Polymers63,0298
Non-polymers00
Water0
1
C: MEF2 CHIMERA
D: MEF2 CHIMERA
G: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
H: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)31,5144
Polymers31,5144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-47 kcal/mol
Surface area14210 Å2
MethodPISA
2
A: MEF2 CHIMERA
B: MEF2 CHIMERA
E: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
F: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)31,5144
Polymers31,5144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-53 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.440, 78.440, 111.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12C
22A
13C
23B
14D
24A
15D
25B
16G
26E
17H
27F
18A
28B

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTHRTHRCA2 - 872 - 87
21GLYGLYTHRTHRDB2 - 872 - 87
12GLYGLYLYSLYSCA2 - 892 - 89
22GLYGLYLYSLYSAE2 - 892 - 89
13GLYGLYLYSLYSCA2 - 892 - 89
23GLYGLYLYSLYSBF2 - 892 - 89
14GLYGLYTHRTHRDB2 - 872 - 87
24GLYGLYTHRTHRAE2 - 872 - 87
15GLYGLYTHRTHRDB2 - 872 - 87
25GLYGLYTHRTHRBF2 - 872 - 87
16DADADGDGGC3 - 142 - 13
26DADADGDGEG2 - 132 - 13
17DTDTDTDTHD2 - 142 - 14
27DTDTDTDTFH3 - 152 - 14
18GLYGLYARGARGAE2 - 902 - 90
28GLYGLYARGARGBF2 - 902 - 90

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
MEF2 CHIMERA / Serum response factor-like protein 1 / RSRFR2 / Serum response factor-like protein 2


Mass: 11327.217 Da / Num. of mol.: 4 / Mutation: D83V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2A, MEF2, MEF2B, XMEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02078, UniProt: Q02080
#2: DNA chain DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')


Mass: 4286.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Mass: 4573.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 3.32 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 5.94, 0.2 M NaCl and 18% PEG2000MME

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.281
11-K, -H, -L20.206
11-h,-k,l30.312
11K, H, -L40.201
ReflectionResolution: 3→67.93 Å / Num. obs: 15258 / % possible obs: 99.73 % / Redundancy: 5.1 % / Net I/σ(I): 41.66
Reflection shellResolution: 3→3.107 Å

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Processing

SoftwareName: REFMAC / Version: 5.8.0189 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→42.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.946 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18997 756 4.8 %RANDOM
Rwork0.13858 ---
obs0.14091 14964 99.65 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.098 Å2
Baniso -1Baniso -2Baniso -3
1-15.42 Å20 Å20 Å2
2--15.42 Å20 Å2
3----30.84 Å2
Refinement stepCycle: 1 / Resolution: 2.97→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 1087 0 0 4026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0174191
X-RAY DIFFRACTIONr_bond_other_d0.0020.023536
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.7275844
X-RAY DIFFRACTIONr_angle_other_deg1.1938237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79123.235136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27915632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4031528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023772
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02841
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8642.9911416
X-RAY DIFFRACTIONr_mcbond_other0.8642.9911415
X-RAY DIFFRACTIONr_mcangle_it1.5034.4851763
X-RAY DIFFRACTIONr_mcangle_other1.5024.4861764
X-RAY DIFFRACTIONr_scbond_it0.823.0892775
X-RAY DIFFRACTIONr_scbond_other0.823.0882774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3434.6214082
X-RAY DIFFRACTIONr_long_range_B_refined3.75455.4315761
X-RAY DIFFRACTIONr_long_range_B_other3.75455.43215760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C50220.07
12D50220.07
21C51140.08
22A51140.08
31C50560.09
32B50560.09
41D50800.06
42A50800.06
51D50240.06
52B50240.06
61G19600.1
62E19600.1
71H21260.14
72F21260.14
81A51360.09
82B51360.09
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 70 -
Rwork0.253 1099 -
obs--99.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.80330.09380.16241.34621.22223.15230.00010.28930.18420.0728-0.0351-0.157-0.22720.21070.0350.2469-0.06260.06140.2560.03860.392777.34748.119-8.755
22.0827-0.24251.33411.85190.16521.81550.03050.0507-0.16640.06060.0321-0.11990.1729-0.1294-0.06260.3544-0.02740.01130.2226-0.01930.352976.28444.02-0.165
35.23862.3393-0.18095.7793-3.24555.0028-0.15470.0957-0.0158-0.41970.08830.2437-0.0352-0.41140.06630.15680.04170.01460.152-0.05940.232759.88854.098-4.99
45.04532.3517-1.33575.5172-0.79474.24560.0737-0.03250.35970.2163-0.05860.3956-0.5868-0.4375-0.01510.16090.02850.00890.131-0.02810.183361.71456.761-3.368
52.2264-0.22520.5121.5391-1.25272.4757-0.06410.02480.14310.12060.1570.17370.0711-0.1744-0.09290.338-0.0941-0.00470.2823-0.00890.458539.57320.011-5.307
60.39430.2325-0.88862.029-0.8893.2624-0.0155-0.12470.04520.13550.0814-0.0189-0.30940.0515-0.06590.33240.01630.00450.298-0.03740.432942.04223.4163.444
71.2557-1.9023-1.36122.90162.05231.4895-0.07-0.27510.28210.01380.3841-0.50220.12370.3563-0.31420.608-0.0233-0.01450.53170.02980.662757.52614.065-1.703
82.03152.22321.79926.08684.00163.22950.2423-0.1225-0.18130.44280.0432-0.53490.32940.5189-0.28550.34890.00440.02830.57470.01090.474257.41312.2630.15
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C2 - 91
2X-RAY DIFFRACTION2D2 - 88
3X-RAY DIFFRACTION3G2 - 15
4X-RAY DIFFRACTION4H2 - 14
5X-RAY DIFFRACTION5A2 - 90
6X-RAY DIFFRACTION6B2 - 90
7X-RAY DIFFRACTION7E2 - 14
8X-RAY DIFFRACTION8F3 - 15

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