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- PDB-3u5v: Crystal structure of Max-E47 -

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Basic information

Entry
Database: PDB / ID: 3u5v
TitleCrystal structure of Max-E47
ComponentsProtein max, Transcription factor E2-alpha chimera
KeywordsTRANSCRIPTION / basic helix-loop-helix (bHLH) / transcription factor
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / vitamin D response element binding / Mad-Max complex / Myc-Max complex / bHLH transcription factor binding / immunoglobulin V(D)J recombination / mitogen-activated protein kinase kinase kinase binding / cellular response to peptide hormone stimulus / B cell lineage commitment / Myogenesis ...Transcriptional Regulation by E2F6 / vitamin D response element binding / Mad-Max complex / Myc-Max complex / bHLH transcription factor binding / immunoglobulin V(D)J recombination / mitogen-activated protein kinase kinase kinase binding / cellular response to peptide hormone stimulus / B cell lineage commitment / Myogenesis / E-box binding / regulation of G1/S transition of mitotic cell cycle / MLL1 complex / response to axon injury / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / positive regulation of B cell proliferation / positive regulation of neuron differentiation / cellular response to starvation / B cell differentiation / protein-DNA complex / euchromatin / response to insulin / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / positive regulation of DNA-binding transcription factor activity / sequence-specific double-stranded DNA binding / retina development in camera-type eye / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / 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 / protein heterodimerization activity / negative regulation of gene expression / dendrite / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 / identical protein binding / nucleus / cytoplasm
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
NITRATE ION / Transcription factor E2-alpha / Protein max
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuarne, A. / Ahmadpour, F. / Gloyd, M.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure of the minimalist max-e47 protein chimera.
Authors: Ahmadpour, F. / Ghirlando, R. / De Jong, A.T. / Gloyd, M. / Shin, J.A. / Guarne, A.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein max, Transcription factor E2-alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2003
Polymers9,0751
Non-polymers1242
Water61334
1
A: Protein max, Transcription factor E2-alpha chimera
hetero molecules

A: Protein max, Transcription factor E2-alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3996
Polymers18,1512
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.480, 49.466, 74.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-701-

NO3

21A-95-

HOH

31A-105-

HOH

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Components

#1: Protein Protein max, Transcription factor E2-alpha chimera / Myc-associated factor X / Myc-binding novel HLH/LZ protein / Protein myn / Immunoglobulin enhancer- ...Myc-associated factor X / Myc-binding novel HLH/LZ protein / Protein myn / Immunoglobulin enhancer-binding factor E47 / Class B basic helix-loop-helix protein 21 / bHLHb21 / Immunoglobulin transcription factor 1 / Kappa-E2-binding factor / Transcription factor 3 / TCF-3 / Transcription factor ITF-1


Mass: 9075.493 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Max, Myn, BHLHB21, E2A, ITF1, TCF3 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28574, UniProt: P15923
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN CONSTRUCT IS A CHIMERA OF THE BASIC REGION OF MURINE MAX (UNP P28574 RESIDUES 22-36) ...THE PROTEIN CONSTRUCT IS A CHIMERA OF THE BASIC REGION OF MURINE MAX (UNP P28574 RESIDUES 22-36) AND THE HELIX-LOOP-HELIX REGION OF HUMAN E47 (UNP P15923-2 RESIDUES 560-610).

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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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% glycerol, 3.2-3.5 M sodium nitrate, 0.1 M sodium acetate anhydrous, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 7877 / Num. obs: 7852 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.044 / Net I/σ(I): 32.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.7-1.734.60.6472.13850.56598.5
1.73-1.765.70.6052.53730.57499.7
1.76-1.797.10.5583.53930.534100
1.79-1.8380.5473.93670.521100
1.83-1.8790.4645.43970.416100
1.87-1.919.50.48663850.455100
1.91-1.969.80.3877.83840.366100
1.96-2.029.90.2969.83970.3100
2.02-2.079.70.242123880.235100
2.07-2.149.90.18516.53770.182100
2.14-2.229.90.13220.63970.131100
2.22-2.319.80.12223980.12100
2.31-2.419.80.10924.93840.111100
2.41-2.549.80.125.23970.099100
2.54-2.79.60.09224.93920.092100
2.7-2.919.50.07626.83890.0899.7
2.91-3.29.30.05934.54080.062100
3.2-3.668.90.041373890.04298.2
3.66-4.619.60.03152.74170.036100
4.61-4090.03446.54350.04197.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QL2

2ql2


Resolution: 1.7→23.256 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 23.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.235 353 4.68 %RANDOM
Rwork0.207 ---
all0.2082 7881 --
obs0.2082 7550 95.8 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.441 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.021 Å20 Å2-0 Å2
2--6.2644 Å2-0 Å2
3----2.7783 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 8 34 548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003514
X-RAY DIFFRACTIONf_angle_d0.567683
X-RAY DIFFRACTIONf_dihedral_angle_d12.619210
X-RAY DIFFRACTIONf_chiral_restr0.03776
X-RAY DIFFRACTIONf_plane_restr0.00193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7-1.94640.30421050.25562217232290
1.9464-2.45180.20841140.19542417253197
2.4518-23.25770.23511340.20382563269799
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)
12.1773-1.19120.98751.3377-0.0574.9955-0.2394-0.43420.24310.7956-0.90490.36470.9717-0.7293-0.00970.6945-0.10450.19230.1837-0.12070.15-4.248722.048931.8696
20.93330.70940.05856.93877.34528.4556-0.12120.09620.50030.3223-0.18511.2345-0.1709-0.77670.17780.21340.02160.04870.2517-0.0080.2402-6.430118.761222.9211
30.13070.04580.06011.76270.92671.83720.02230.09750.1309-0.1585-0.0070.60210.0429-0.71190.12970.1312-0.0383-0.04010.26320.02110.2582-7.792511.826212.4924
43.4425-0.1535-3.20211.72861.58646.1705-0.6488-0.10560.5728-0.4377-0.19770.46870.6121-0.9288-0.32830.2495-0.0894-0.15290.49330.0870.3601-8.49574.82534.3163
53.82671.98181.47052.35231.34511.8953-0.1353-0.18020.0001-0.51710.15880.53890.2047-0.656-0.07380.3335-0.1059-0.06850.30010.05040.1893-6.44221.515214.1082
60.72740.1205-0.0552-0.0816-0.35084.53470.0342-0.0038-0.01280.00830.0164-0.11120.69950.1087-0.030.2121-0.0014-0.01640.1746-0.00230.15621.14846.41518.7868
71.17671.45930.36471.9888-0.37054.7363-0.03040.3635-0.10710.05020.1479-0.5343-0.42850.7633-0.26970.1327-0.01130.06390.389-0.06830.20923.92528.526-5.8016
82.06330.6969-2.78414.28630.37694.2736-0.12120.008-0.1297-0.3087-0.4209-1.41140.0395-0.4820.15750.40450.2093-0.03130.96450.17480.6291-3.20297.0876-15.6925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:12)
2X-RAY DIFFRACTION2(chain A and resid 13:20)
3X-RAY DIFFRACTION3(chain A and resid 21:29)
4X-RAY DIFFRACTION4(chain A and resid 30:34)
5X-RAY DIFFRACTION5(chain A and resid 35:41)
6X-RAY DIFFRACTION6(chain A and resid 42:54)
7X-RAY DIFFRACTION7(chain A and resid 55:61)
8X-RAY DIFFRACTION8(chain A and resid 62:68)

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