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- PDB-1mdy: CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ... -

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Basic information

Entry
Database: PDB / ID: 1mdy
TitleCRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION
Components
  • (PROTEIN (MYOD BHLH DOMAIN)) x 2
  • DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


myoblast fate determination / negative regulation of chromatin binding / nuclear receptor binding => GO:0016922 / negative regulation of myoblast proliferation / myotube differentiation involved in skeletal muscle regeneration / positive regulation of snRNA transcription by RNA polymerase II / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / : / positive regulation of binding / skeletal muscle fiber adaptation ...myoblast fate determination / negative regulation of chromatin binding / nuclear receptor binding => GO:0016922 / negative regulation of myoblast proliferation / myotube differentiation involved in skeletal muscle regeneration / positive regulation of snRNA transcription by RNA polymerase II / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / : / positive regulation of binding / skeletal muscle fiber adaptation / myotube differentiation / : / positive regulation of skeletal muscle fiber development / muscle cell differentiation / positive regulation of skeletal muscle tissue regeneration / myotube cell development / bHLH transcription factor binding / skeletal muscle tissue regeneration / cellular response to oxygen levels / cardiac muscle cell differentiation / Myogenesis / myoblast fusion / cellular response to glucocorticoid stimulus / myoblast differentiation / muscle organ development / DNA-binding transcription activator activity / regulation of alternative mRNA splicing, via spliceosome / myofibril / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / E-box binding / skeletal muscle cell differentiation / regulation of RNA splicing / transcription factor binding / positive regulation of myoblast differentiation / cis-regulatory region sequence-specific DNA binding / skeletal muscle fiber development / skeletal muscle tissue development / striated muscle cell differentiation / cellular response to starvation / cellular response to estradiol stimulus / promoter-specific chromatin binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / euchromatin / chromatin DNA binding / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / regulation of gene expression / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Myogenic muscle-specific protein, N-terminal / Myogenic determination factor 5 / Myogenic factor / Myogenic Basic domain / Myogenic determination factor 5 / Basic domain in HLH proteins of MYOD family / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily ...Myogenic muscle-specific protein, N-terminal / Myogenic determination factor 5 / Myogenic factor / Myogenic Basic domain / Myogenic determination factor 5 / Basic domain in HLH proteins of MYOD family / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Myoblast determination protein 1 / Myoblast determination protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMa, P.C.M. / Rould, M.A. / Weintraub, H. / Pabo, C.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1994
Title: Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation.
Authors: Ma, P.C. / Rould, M.A. / Weintraub, H. / Pabo, C.O.
History
DepositionJun 9, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
F: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
G: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
H: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
A: PROTEIN (MYOD BHLH DOMAIN)
B: PROTEIN (MYOD BHLH DOMAIN)
C: PROTEIN (MYOD BHLH DOMAIN)
D: PROTEIN (MYOD BHLH DOMAIN)


Theoretical massNumber of molelcules
Total (without water)46,9868
Polymers46,9868
Non-polymers00
Water45025
1
E: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
F: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
A: PROTEIN (MYOD BHLH DOMAIN)
B: PROTEIN (MYOD BHLH DOMAIN)


Theoretical massNumber of molelcules
Total (without water)23,8874
Polymers23,8874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
H: DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')
C: PROTEIN (MYOD BHLH DOMAIN)
D: PROTEIN (MYOD BHLH DOMAIN)


Theoretical massNumber of molelcules
Total (without water)23,0984
Polymers23,0984
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.800, 70.800, 30.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.645814, 0.72052, -0.252539), (0.74446, 0.667667, 0.001127), (0.169423, -0.187277, -0.967586)102.97015, -45.90718, 11.36556
2given(-0.533164, 0.834325, 0.140135), (0.807272, 0.551272, -0.210739), (-0.253077, 0.000768, -0.967446)173.68367, -90.34569, 34.22189
DetailsTHE ASYMMETRIC UNIT CONTAINS FOUR MONOMERS OF MYOD TOGETHER WITH TWO DOUBLE-STRANDED 14 BASE PAIR OLIGONUCLEOTIDES. THERE ARE, THUS, TWO HOMODIMERS OF MYOD BOUND TO TWO DNA SITES IN THE ASYMMETRIC UNIT. THE DEPOSITORS HAVE INCLUDED RESIDUES 105 - 166 OF ALL FOUR OF THE MYOD MONOMERS IN THEIR MODEL. RESIDUES 1 - 3 AND 102 - 104 ARE ALSO INCLUDED IN ONE OUT OF THE FOUR MONOMERS, WHERE THESE RESIDUES ARE INVOLVED IN CRYSTAL PACKING CONTACTS. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *C*.

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Components

#1: DNA chain
DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')


Mass: 4279.804 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein PROTEIN (MYOD BHLH DOMAIN)


Mass: 8058.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: MYOD_MOUSE, UniProt: P10085*PLUS
#3: Protein PROTEIN (MYOD BHLH DOMAIN)


Mass: 7269.341 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P10085*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDNA SYNTHETIC OLIGONUCLEOTIDE OF 14 BASE PAIRS, CONTAINING THE OPTIMIZED DNA BINDING SITE FOR THE ...DNA SYNTHETIC OLIGONUCLEOTIDE OF 14 BASE PAIRS, CONTAINING THE OPTIMIZED DNA BINDING SITE FOR THE MYOD HOMODIMER: 5'-(TCAACAGCTGTTGA)-3'.
Sequence detailsTHE PROTEIN RESIDUES ARE NUMBERED ACCORDING TO THE NATIVE SCHEME FOR MOUSE MYOD PROTEIN. THERE ARE ...THE PROTEIN RESIDUES ARE NUMBERED ACCORDING TO THE NATIVE SCHEME FOR MOUSE MYOD PROTEIN. THERE ARE FOUR SEPARATE MYOD MONOMERS IN THE ASYMMETRIC UNIT, WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A, B, C, AND D. MONOMER A FORMS A DIMER WITH MONOMER B; MONOMER C FORMS A DIMER WITH MONOMER D. THERE ARE FOUR DNA STRANDS IN THE ASYMMETRIC UNIT, WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS E, F, G, AND H. STRAND E FORMS A DOUBLE STRAND WITH F, WHILE G AND H FORM THE OTHER DOUBLE STRAND. MYOD DIMER AB IS BOUND TO DNA DOUBLE STRAND EF. MYOD DIMER CD IS BOUND TO DNA DOUBLE STRAND GH.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 %PEG35001drop
2100 mMTris-HCl1drop
3100 mMNa-citrate1drop
420 mM1dropBaCl2

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORrefinement
TNTrefinement
RefinementRfactor Rfree: 0.33 / Rfactor Rwork: 0.253 / Rfactor obs: 0.253 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 1136 0 25 3247
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. reflection all: 10585 / Num. reflection obs: 8963 / σ(I): 2 / Rfactor obs: 0.224 / Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS

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