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- PDB-6c9l: MEF2B Apo Protein Structure -

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Basic information

Entry
Database: PDB / ID: 6c9l
TitleMEF2B Apo Protein Structure
ComponentsMyocyte-specific enhancer factor 2B
KeywordsTRANSCRIPTION / MEF2 / MEF2B / MEF2B Apo Structure / Self-regulatory protein
Function / homology
Function and homology information


muscle organ development / Myogenesis / histone deacetylase binding / sequence-specific double-stranded DNA binding / cell junction / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / protein dimerization activity ...muscle organ development / Myogenesis / histone deacetylase binding / sequence-specific double-stranded DNA binding / cell junction / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
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
Myocyte-specific enhancer factor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Biochemistry / Year: 2018
Title: Crystal Structure of Apo MEF2B Reveals New Insights in DNA Binding and Cofactor Interaction.
Authors: Lei, X. / Shi, H. / Kou, Y. / Rajashekar, N. / Wu, F. / Sen, C. / Xu, J. / Chen, L.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / 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 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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_alt_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: Myocyte-specific enhancer factor 2B
B: Myocyte-specific enhancer factor 2B
C: Myocyte-specific enhancer factor 2B
D: Myocyte-specific enhancer factor 2B
E: Myocyte-specific enhancer factor 2B
F: Myocyte-specific enhancer factor 2B


Theoretical massNumber of molelcules
Total (without water)66,2336
Polymers66,2336
Non-polymers00
Water2,126118
1
A: Myocyte-specific enhancer factor 2B
B: Myocyte-specific enhancer factor 2B


Theoretical massNumber of molelcules
Total (without water)22,0782
Polymers22,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-46 kcal/mol
Surface area9990 Å2
MethodPISA
2
C: Myocyte-specific enhancer factor 2B
D: Myocyte-specific enhancer factor 2B


Theoretical massNumber of molelcules
Total (without water)22,0782
Polymers22,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-45 kcal/mol
Surface area10120 Å2
MethodPISA
3
E: Myocyte-specific enhancer factor 2B
F: Myocyte-specific enhancer factor 2B


Theoretical massNumber of molelcules
Total (without water)22,0782
Polymers22,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-33 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.780, 178.490, 43.410
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label alt-ID
11GLNGLNLYSLYSAA7 - 897 - 89
21GLNGLNLYSLYSBB7 - 897 - 89
12GLNGLNLEULEUAA7 - 887 - 88
22GLNGLNLEULEUCC7 - 887 - 88
13GLNGLNARGARGAA7 - 907 - 90
23GLNGLNARGARGDD7 - 907 - 90
14SERSERGLUGLUAA9 - 719 - 71
24SERSERGLUGLUEE9 - 719 - 71
15ILEILELYSLYSAA8 - 898 - 89
25ILEILELYSLYSFF8 - 898 - 89P
16ILEILELEULEUBB6 - 886 - 88
26ILEILELEULEUCC6 - 886 - 88
17GLNGLNLYSLYSBB7 - 897 - 89
27GLNGLNLYSLYSDD7 - 897 - 89
18SERSERGLUGLUBB9 - 719 - 71
28SERSERGLUGLUEE9 - 719 - 71
19ILEILELYSLYSBB8 - 898 - 89
29ILEILELYSLYSFF8 - 898 - 89P
110GLNGLNLEULEUCC7 - 887 - 88
210GLNGLNLEULEUDD7 - 887 - 88
111SERSERGLUGLUCC9 - 719 - 71
211SERSERGLUGLUEE9 - 719 - 71
112ILEILELYSLYSCC8 - 898 - 89
212ILEILELYSLYSFF8 - 898 - 89P
113SERSERGLUGLUDD9 - 719 - 71
213SERSERGLUGLUEE9 - 719 - 71
114ILEILELYSLYSDD8 - 898 - 89
214ILEILELYSLYSFF8 - 898 - 89P
115SERSERGLUGLUEE9 - 719 - 71
215SERSERGLUGLUFF9 - 719 - 71

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Myocyte-specific enhancer factor 2B / RSRFR2 / Serum response factor-like protein 2


Mass: 11038.855 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2B, XMEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02080
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.4 M NaCl, 0.1 M Bis-Tris pH 5.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→89.25 Å / Num. obs: 23268 / % possible obs: 98 % / Redundancy: 2.7 % / Net I/σ(I): 8.5
Reflection shellResolution: 2.331→2.39 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→89.24 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 15.412 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23482 1071 4.7 %RANDOM
Rwork0.21483 ---
obs0.21577 21947 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 35.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-0.09 Å2
2---0.66 Å2-0 Å2
3---1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.3→89.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 0 118 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194029
X-RAY DIFFRACTIONr_bond_other_d0.0020.023887
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9725403
X-RAY DIFFRACTIONr_angle_other_deg138977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12523.134201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5141543
X-RAY DIFFRACTIONr_chiral_restr0.0870.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
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_it0.531.5181909
X-RAY DIFFRACTIONr_mcbond_other0.531.5171908
X-RAY DIFFRACTIONr_mcangle_it0.9462.2672374
X-RAY DIFFRACTIONr_mcangle_other0.9462.2682375
X-RAY DIFFRACTIONr_scbond_it0.5521.6012120
X-RAY DIFFRACTIONr_scbond_other0.5521.6022121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9362.3753030
X-RAY DIFFRACTIONr_long_range_B_refined3.07317.5384499
X-RAY DIFFRACTIONr_long_range_B_other3.02717.474484
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)
11A46560.15
12B46560.15
21A46100.15
22C46100.15
31A50440.08
32D50440.08
41A37940.09
42E37940.09
51A44720.12
52F44720.12
61B48700.09
62C48700.09
71B46200.15
72D46200.15
81B36220.13
82E36220.13
91B42980.16
92F42980.16
101C45780.15
102D45780.15
111C36660.12
112E36660.12
121C42980.16
122F42980.16
131D37900.09
132E37900.09
141D44360.12
142F44360.12
151E38360.08
152F38360.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 54 -
Rwork0.264 1642 -
obs--99.65 %
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)
12.2548-0.75430.08334.832-0.21591.17570.0068-0.0489-0.12050.1706-0.03350.0472-0.0330.05850.02670.0091-0.0108-0.00140.0349-0.00530.10958.458-17.3134.424
24.2309-0.9669-0.69482.87360.14352.1721-0.01280.27970.0024-0.0965-0.0210.07560.004-0.08320.03380.0361-0.0159-0.02070.02540.00620.10264.968-13.00833.038
34.89530.82950.0012.5440.02571.1905-0.0265-0.2830.01180.11640.0071-0.0753-0.0227-0.08140.01930.05740.032-0.01690.0378-00.1038-7.7069.74411.117
42.72730.298-0.1194.5526-0.37910.64230.0430.08660.168-0.1544-0.05940.0520.05080.05180.01630.02470.0132-0.0250.0569-0.01350.114-4.02114.3459.57
56.2713-1.21981.69454.7552-1.56222.01930.24740.1839-0.0479-0.3598-0.2221-0.0942-0.0956-0.0611-0.02530.2146-0.0385-0.03230.10090.00680.275813.53844.1923.951
66.5651-1.1614-1.00135.29070.57211.9180.0009-0.1039-0.211-0.01010.00370.0671-0.00590.1499-0.00450.1528-0.08710.01640.0621-0.0220.29674.92542.1936.58
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 90
2X-RAY DIFFRACTION2B6 - 90
3X-RAY DIFFRACTION3C5 - 89
4X-RAY DIFFRACTION4D7 - 90
5X-RAY DIFFRACTION5E9 - 72
6X-RAY DIFFRACTION6F8 - 89

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