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- PDB-5eyo: The crystal structure of the Max bHLH domain in complex with 5-ca... -

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Basic information

Entry
Database: PDB / ID: 5eyo
TitleThe crystal structure of the Max bHLH domain in complex with 5-carboxyl cytosine DNA
Components
  • DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')
  • Protein max
KeywordsTRANSCRIPTION/DNA / bHLH protein / 5-carboxylcytosine DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / dendrite / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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) / Protein max
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsWang, D. / Hashimoto, H. / Zhang, X. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma.
Authors: Wang, D. / Hashimoto, H. / Zhang, X. / Barwick, B.G. / Lonial, S. / Boise, L.H. / Vertino, P.M. / Cheng, X.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein max
B: DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')
C: Protein max
D: DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,8684
Polymers30,8684
Non-polymers00
Water19811
1
A: Protein max
B: DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')

A: Protein max
B: DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,8684
Polymers30,8684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7780 Å2
ΔGint-60 kcal/mol
Surface area15240 Å2
MethodPISA
2
C: Protein max
D: DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')

C: Protein max
D: DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,8684
Polymers30,8684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7490 Å2
ΔGint-68 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.750, 306.160, 49.060
Angle α, β, γ (deg.)90.00, 103.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein max / Class D basic helix-loop-helix protein 4 / bHLHd4 / Myc-associated factor X


Mass: 10491.827 Da / Num. of mol.: 2 / Fragment: UNP residues 22-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293T cells / Gene: MAX, BHLHD4 / Plasmid: pET-His-sumo / Details (production host): pXC1407 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: P61244
#2: DNA chain DNA (5'-D(*AP*GP*TP*AP*GP*CP*AP*(1CC)P*GP*TP*GP*CP*TP*AP*CP*T)-3')


Mass: 4942.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 1CC is 5-carboxy-2'-deoxycytidine monophosphate / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.87 Å3/Da / Density % sol: 68.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium Sulfate, 0.1 M Sodium Citrate-HCl pH 5.6, 25% (w/v) PEG 4000
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→38.27 Å / Num. obs: 18442 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 60.34 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.7
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11_2558: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AN2

1an2


Resolution: 2.39→38.27 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 908 4.97 %Random selection
Rwork0.2032 ---
obs0.2045 18257 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 656 0 11 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032155
X-RAY DIFFRACTIONf_angle_d0.5463041
X-RAY DIFFRACTIONf_dihedral_angle_d20.5391207
X-RAY DIFFRACTIONf_chiral_restr0.03331
X-RAY DIFFRACTIONf_plane_restr0.002290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3901-2.53980.37531480.34212862X-RAY DIFFRACTION98
2.5398-2.73590.32421530.28992910X-RAY DIFFRACTION98
2.7359-3.01110.33681500.26562879X-RAY DIFFRACTION100
3.0111-3.44660.25731490.23332843X-RAY DIFFRACTION98
3.4466-4.34130.1981530.18612920X-RAY DIFFRACTION100
4.3413-38.27490.19611550.1672935X-RAY DIFFRACTION100
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)
14.64.38212.54094.31662.97153.5494-0.51910.7678-0.7215-1.08670.8605-0.69681.7655-0.6619-0.35521.77480.094-0.00360.7517-0.10.645-2.462111.350411.5523
25.7431-3.4739-4.78064.27235.78397.86170.1511-0.02440.7489-0.23440.4793-2.36910.17231.1411-0.63081.0410.0011-0.19860.3837-0.05330.84661.757833.746722.3327
35.6756-2.668-3.55912.27472.73533.3550.2124-0.75280.77051.1360.6061-0.37430.03920.2282-0.75721.18230.0499-0.18730.341-0.00020.7718-4.927239.628629.9431
40.7328-1.9443-0.29175.4476-0.67746.69910.0828-0.23910.92310.2155-0.07360.40030.6216-0.01960.24910.3557-0.04360.21050.46450.05931.491-10.294463.684624.8305
51.53152.37511.83038.4833-2.77948.7714-0.10040.42350.722-1.1728-0.4357-1.0381-0.68470.54340.38070.7073-0.03550.23860.36930.10262.4501-8.752187.299620.1058
67.575-1.09468.66570.1603-1.222.00180.6004-1.4351-0.73081.44220.48660.54080.9673-0.70290.13111.8618-0.1292-0.41051.049-0.00350.4786-1.537417.874642.9701
73.43440.73682.31.59673.25876.97110.39370.2943-0.3752-0.43630.2222-0.2918-0.2968-0.2547-0.24921.67840.0268-0.50310.58970.00650.4907-4.193516.601422.7616
85.7031.4898-6.08811.8652-0.88077.80680.89290.54330.51771.3742-0.64340.0883-3.3752-0.30430.70091.83590.2322-0.35891.10310.03910.5783-17.993621.02268.0098
95.96886.54375.42798.48655.28235.279-1.5483-0.4452.8965-0.3458-0.0058-1.2375-2.02930.5241.47251.902-0.2155-0.21910.646-0.011.22455.5392.859131.2326
105.71052.99632.06836.751-1.33082.011-0.56840.4516-1.0436-0.7940.4305-0.6354-0.61180.9180.1461.2251-0.18280.12390.4709-0.11370.81212.4092-20.12623.0095
110.7599-1.57571.60165.6654-2.18043.8686-0.08560.5989-1.6327-1.85840.4233-0.54890.5455-0.1173-0.00991.19090.0567-0.06430.4378-0.18361.3203-8.8347-34.340618.9185
123.0874-1.14090.46142.1283-3.1275.21470.0964-0.11280.37851.2068-0.4235-0.326-0.75430.02810.35680.6783-0.088-0.04320.46110.00941.6873-8.3403-65.497327.4943
130.6882-1.4524-2.48743.06365.25139.0042-0.4008-0.3474-0.15711.3185-0.2109-0.63191.07290.3920.49850.5954-0.03380.06120.31920.0661.9988-4.167-87.255228.1596
147.54120.0451-1.40918.3613-3.1977.92810.16522.1916-0.66750.20880.19740.9938-1.7102-0.1344-0.22741.75010.1028-0.2660.9067-0.1230.5659-16.9369-9.9427.5941
156.81126.17455.92557.85727.51927.56630.25860.0847-0.46950.25520.1633-0.4885-0.84170.1831-0.44481.3878-0.0907-0.07170.49390.01620.4423-3.5341-10.324519.7056
165.8826-0.50541.46494.4615-3.56933.05450.0281-1.2346-0.76820.09640.38910.0683-1.5389-0.2966-0.44011.71360.0232-0.04910.97920.05920.4544-3.4435-10.128940.4794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 20:33)
2X-RAY DIFFRACTION2(chain A and resid 34:56)
3X-RAY DIFFRACTION3(chain A and resid 57:73)
4X-RAY DIFFRACTION4(chain A and resid 74:93)
5X-RAY DIFFRACTION5(chain A and resid 94:105)
6X-RAY DIFFRACTION6(chain B and resid 4:7)
7X-RAY DIFFRACTION7(chain B and resid 8:15)
8X-RAY DIFFRACTION8(chain B and resid 16:19)
9X-RAY DIFFRACTION9(chain C and resid 20:25)
10X-RAY DIFFRACTION10(chain C and resid 26:52)
11X-RAY DIFFRACTION11(chain C and resid 53:78)
12X-RAY DIFFRACTION12(chain C and resid 79:100)
13X-RAY DIFFRACTION13(chain C and resid 101:107)
14X-RAY DIFFRACTION14(chain D and resid 4:7)
15X-RAY DIFFRACTION15(chain D and resid 8:13)
16X-RAY DIFFRACTION16(chain D and resid 14:19)

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