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- PDB-6wc5: Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DN... -

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Basic information

Entry
Database: PDB / ID: 6wc5
TitleCrystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA Complex
Components
  • (Myocardin enhancer DNA) x 2
  • Homeobox protein Nkx-2.5
  • Myocyte-specific enhancer factor 2B
KeywordsTRANSCRIPTION / transcription complex / Cardiogenesis / Carcinogenesis / MADS-box and Homeobox
Function / homology
Function and homology information


Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / Nkx-2.5 complex / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / bundle of His development ...Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / Nkx-2.5 complex / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / bundle of His development / atrial cardiac muscle cell development / ventricular cardiac myofibril assembly / atrioventricular node cell development / embryonic heart tube left/right pattern formation / positive regulation of cardioblast differentiation / atrial cardiac muscle tissue development / atrioventricular node development / regulation of cardiac muscle cell proliferation / atrial septum morphogenesis / positive regulation of heart contraction / ventricular cardiac muscle cell development / negative regulation of myotube differentiation / Physiological factors / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / pharyngeal system development / positive regulation of sodium ion transport / negative regulation of epithelial cell apoptotic process / ventricular trabecula myocardium morphogenesis / adult heart development / heart trabecula formation / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / embryonic heart tube development / aortic valve morphogenesis / Cardiogenesis / cardiac muscle cell development / epithelial cell apoptotic process / negative regulation of cardiac muscle cell apoptotic process / cardiac muscle cell proliferation / muscle organ development / DNA-binding transcription activator activity / ventricular septum morphogenesis / Myogenesis / cardiac septum morphogenesis / heart looping / thyroid gland development / hemopoiesis / regulation of cardiac conduction / regulation of cardiac muscle contraction / positive regulation of transcription initiation by RNA polymerase II / heart morphogenesis / vasculogenesis / cardiac muscle contraction / spleen development / epithelial cell differentiation / positive regulation of neuron differentiation / positive regulation of epithelial cell proliferation / epithelial cell proliferation / negative regulation of canonical Wnt signaling pathway / protein-DNA complex / RNA polymerase II transcription regulator complex / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / 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 / Homeobox domain, metazoa / Homeobox, conserved site ...: / 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 / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein Nkx-2.5 / Myocyte-specific enhancer factor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChen, L. / Lei, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5U54DK107981 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.
Authors: Lei, X. / Zhao, J. / Sagendorf, J.M. / Rajashekar, N. / Xu, J. / Dantas Machado, A.C. / Sen, C. / Rohs, R. / Feng, P. / Chen, L.
History
DepositionMar 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
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: Myocardin enhancer DNA
F: Myocardin enhancer DNA
G: Myocardin enhancer DNA
H: Myocardin enhancer DNA
I: Homeobox protein Nkx-2.5
N: Homeobox protein Nkx-2.5


Theoretical massNumber of molelcules
Total (without water)84,03610
Polymers84,03610
Non-polymers00
Water543
1
A: Myocyte-specific enhancer factor 2B
B: Myocyte-specific enhancer factor 2B
E: Myocardin enhancer DNA
F: Myocardin enhancer DNA
I: Homeobox protein Nkx-2.5


Theoretical massNumber of molelcules
Total (without water)42,0185
Polymers42,0185
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-76 kcal/mol
Surface area18170 Å2
MethodPISA
2
C: Myocyte-specific enhancer factor 2B
D: Myocyte-specific enhancer factor 2B
G: Myocardin enhancer DNA
H: Myocardin enhancer DNA
N: Homeobox protein Nkx-2.5


Theoretical massNumber of molelcules
Total (without water)42,0185
Polymers42,0185
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-78 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.040, 93.240, 136.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27G
18F
28H
19I
29N

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-ID
11GLYGLYLYSLYSAA2 - 891 - 88
21GLYGLYLYSLYSBB2 - 891 - 88
12GLYGLYLYSLYSAA2 - 891 - 88
22GLYGLYLYSLYSCC2 - 891 - 88
13GLYGLYLYSLYSAA2 - 891 - 88
23GLYGLYLYSLYSDD2 - 891 - 88
14GLYGLYARGARGBB2 - 911 - 90
24GLYGLYARGARGCC2 - 911 - 90
15GLYGLYARGARGBB2 - 911 - 90
25GLYGLYARGARGDD2 - 911 - 90
16GLYGLYARGARGCC2 - 911 - 90
26GLYGLYARGARGDD2 - 911 - 90
17DADADTDTEE1 - 201 - 20
27DADADTDTGG1 - 201 - 20
18DCDCDTDTFF1 - 202 - 21
28DCDCDTDTHH1 - 202 - 21
19ARGARGSERSERII142 - 1933 - 54
29ARGARGSERSERNJ142 - 1933 - 54

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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


Mass: 10737.450 Da / Num. of mol.: 4
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: DNA chain Myocardin enhancer DNA


Mass: 6774.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Myocardin enhancer DNA


Mass: 6725.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein Homeobox protein Nkx-2.5 / Cardiac-specific homeobox / Homeobox protein CSX / Homeobox protein NK-2 homolog E


Mass: 7043.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NKX2-5, CSX, NKX2.5, NKX2E / Production host: Escherichia coli (E. coli) / References: UniProt: P52952
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 100 mM HEPES pH 7.0, 18% PEG 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.032 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.032 Å / Relative weight: 1
ReflectionResolution: 2.9→77 Å / Num. obs: 18336 / % possible obs: 94.29 % / Redundancy: 4.1 % / CC1/2: 0.997 / Net I/σ(I): 11.32
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 1904 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N6J

1n6j


Resolution: 2.9→76.99 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 39.751 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 884 4.8 %RANDOM
Rwork0.2052 ---
obs0.2074 17451 94.89 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 175.13 Å2 / Biso mean: 70.396 Å2 / Biso min: 15.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0 Å2
2---0.18 Å20 Å2
3---1.29 Å2
Refinement stepCycle: final / Resolution: 2.9→76.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 1751 0 3 5706
Biso mean---23.72 -
Num. residues----555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125967
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184894
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.4898376
X-RAY DIFFRACTIONr_angle_other_deg1.2231.87811360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.18219.73259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88915828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2061554
X-RAY DIFFRACTIONr_chiral_restr0.1530.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021340
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23850.16
12B23850.16
21A24390.13
22C24390.13
31A23880.15
32D23880.15
41B24660.17
42C24660.17
51B24710.15
52D24710.15
61C24670.15
62D24670.15
71E18260.02
72G18260.02
81F17740.05
82H17740.05
91I16110.18
92N16110.18
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 66 -
Rwork0.343 1325 -
all-1391 -
obs--99.71 %
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)
14.3135-0.3188-1.75856.4290.7364.4470.04350.24050.50070.24360.3091-0.2216-0.1691-0.1139-0.35260.30790.0063-0.05890.42290.14960.1231-22.662-9.108-3.377
24.9895-0.0873-1.99793.5027-1.3165.32850.02450.2470.31670.13070.25750.4786-0.1803-0.3907-0.28190.38820.0345-0.01350.33910.0980.1304-27.691-8.4221.278
33.7405-0.70180.44264.9975-1.56463.9925-0.21720.0963-0.5029-0.08480.07750.28610.1271-0.0130.13970.3362-0.00770.04380.2303-0.02660.0959-45.78613.713-27.506
45.2930.15552.14356.00460.59924.8144-0.24140.121-0.4013-0.0420.1797-0.2410.18860.18520.06170.30380.05820.10650.17930.03770.0784-40.83411.681-23.02
51.22080.0714-0.91470.89440.82478.42830.14990.0141-0.13240.06170.2525-0.12720.24220.2945-0.40240.41840.008-0.04670.33070.01850.0646-25.05-25.05512.323
61.3723-0.5408-2.16041.70270.04016.96030.03550.03480.05640.05210.2218-0.16140.2699-0.0833-0.25730.4504-0.04330.00060.33360.00590.0429-25.109-24.99612.783
71.0914-0.29361.92071.1378-0.881110.1240.08760.04120.06010.01520.1086-0.1409-0.3618-0.0157-0.19620.402-0.0167-0.0140.3201-0.02510.0418-38.42728.247-14.539
80.9841-0.25872.10781.6443-0.99548.5784-0.0048-0.02480.03110.01390.104-0.133-0.02140.4134-0.09930.3297-0.0341-0.03930.335-0.02290.0258-38.54527.708-13.94
96.7008-1.51480.45838.6492-0.15936.6714-0.06390.0164-0.37890.2225-0.00140.22520.2442-0.20290.06540.36010.05560.04830.1709-0.0030.0294-32.688-33.60729.651
105.18062.56150.56977.732-0.50474.522-0.12740.14010.3573-0.13580.0302-0.8393-0.35310.14170.09720.48280.0529-0.18550.3729-0.11330.334-29.20735.5774.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2B2 - 91
3X-RAY DIFFRACTION3C2 - 91
4X-RAY DIFFRACTION4D2 - 91
5X-RAY DIFFRACTION5E1 - 21
6X-RAY DIFFRACTION6F1 - 21
7X-RAY DIFFRACTION7G1 - 22
8X-RAY DIFFRACTION8H0 - 21
9X-RAY DIFFRACTION9I142 - 196
10X-RAY DIFFRACTION10N140 - 194

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