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- PDB-7rjp: Crystal structure of human Bromodomain containing protein 4 (BRD4... -

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Basic information

Entry
Database: PDB / ID: 7rjp
TitleCrystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT
Components
  • Bromodomain-containing protein 4
  • Serine hydroxymethyltransferase, cytosolic
KeywordsSIGNALING PROTEIN / Brd4 / SHMT / acetyllysine
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / small molecule binding / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / folic acid metabolic process / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / mRNA regulatory element binding translation repressor activity / condensed nuclear chromosome / cellular response to leukemia inhibitory factor / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / mRNA 5'-UTR binding / p53 binding / pyridoxal phosphate binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / protein homotetramerization / Potential therapeutics for SARS / transcription coactivator activity / negative regulation of translation / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / 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 / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / : ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / : / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsFedorov, E. / Islam, K. / Ghosh, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123234 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130752 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM118303 United States
CitationJournal: To Be Published
Title: Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization
Authors: Wagner, S. / Fedorov, E. / Sudhamalla, B. / Jnawali, H.N. / Debiec, R. / Ghosh, A. / Islam, K.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,33816
Polymers15,8582
Non-polymers48014
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-108 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.043, 51.560, 57.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: O60885
#2: Protein/peptide Serine hydroxymethyltransferase, cytosolic / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 758.887 Da / Num. of mol.: 1 / Fragment: UNP residues 270-275 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P34896, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 225 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2020
RadiationMonochromator: KB MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. obs: 45981 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Χ2: 0.893 / Net I/σ(I): 9.6 / Num. measured all: 324543
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.176.90.42222830.9180.1720.4561.03599.9
1.17-1.1970.3822690.9390.1540.4111.008100
1.19-1.2170.35422540.950.1430.3820.993100
1.21-1.2470.33122780.9530.1340.3580.973100
1.24-1.2770.30822950.9620.1240.3320.966100
1.27-1.37.10.27522560.9670.1110.2970.934100
1.3-1.337.10.2522860.9720.10.270.919100
1.33-1.367.10.21622860.9790.0870.2330.864100
1.36-1.47.10.20222770.9830.0810.2180.849100
1.4-1.457.20.17622760.9870.070.1890.817100
1.45-1.57.20.14222970.9910.0560.1530.736100
1.5-1.567.20.1222860.9920.0470.1290.695100
1.56-1.637.20.11123040.9920.0440.1190.657100
1.63-1.727.20.11423200.9910.0450.1230.768100
1.72-1.837.30.12822810.9880.0510.1380.995100
1.83-1.9770.12423330.9890.050.1341.133100
1.97-2.167.30.09923290.9930.0390.1070.986100
2.16-2.487.30.06323360.9970.0250.0680.985100
2.48-3.127.20.04423760.9980.0180.0470.765100
3.12-305.90.04123590.9970.0190.0450.78294

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3940refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXF

3mxf


Resolution: 1.25→25.07 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1738 1819 5.07 %
Rwork0.1484 34055 -
obs0.1497 35874 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.64 Å2 / Biso mean: 11.789 Å2 / Biso min: 3.11 Å2
Refinement stepCycle: final / Resolution: 1.25→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 36 214 1359
Biso mean--30.39 18.86 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.280.1871360.166426032739100
1.28-1.320.17561480.162225632711100
1.32-1.360.16391210.150326122733100
1.36-1.410.15371460.149825782724100
1.41-1.470.1711300.148826142744100
1.47-1.540.1921270.138326152742100
1.54-1.620.15281460.138426022748100
1.62-1.720.14951530.134926282781100
1.72-1.850.1881470.150526002747100
1.85-2.040.17111520.151626212773100
2.04-2.330.16151340.138226592793100
2.33-2.940.16421220.147427002822100
2.94-25.070.19281570.15572660281795
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)
15.7786-1.5937-2.7025.5461-0.18034.50220.10910.0399-0.04720.0713-0.0370.3103-0.2456-0.4462-0.04780.06020.0103-0.01920.1039-0.0060.054-20.9736-13.65667.8448
21.1334-0.3591-0.26940.55540.32241.2517-0.0377-0.0946-0.04950.04040.00760.0380.0663-0.0330.03630.0471-0.01910.00240.0250.00560.0522-6.4419-18.759811.7572
31.952-1.01130.39374.1797-0.80543.0401-0.022-0.06730.15590.0052-0.06160.187-0.2352-0.18550.05490.05390.0032-0.02270.046-0.02640.0679-15.3487-6.151611.1881
41.2957-0.4434-0.82270.73160.37282.83620.01690.0209-0.1007-0.0209-0.03560.00170.04450.0420.02050.03150.0036-0.00330.0252-0.00070.0355-3.4963-17.81274.4328
51.4328-0.3529-0.00551.71430.42111.79780.0053-0.1395-0.00130.0984-0.03560.0499-0.08170.00080.03390.0423-0.01910.00130.0409-0.00480.0442-7.4105-7.709220.0554
62.3414-0.5878-3.01230.59531.10116.25590.0046-0.1882-0.0374-0.07480.0069-0.0497-0.13970.319-0.05050.0518-0.0191-0.00140.07120.0090.06087.1507-14.209514.1644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 42:49)A42 - 49
2X-RAY DIFFRACTION2(chain A and resid 50:98)A50 - 98
3X-RAY DIFFRACTION3(chain A and resid 99:105)A99 - 105
4X-RAY DIFFRACTION4(chain A and resid 106:126)A106 - 126
5X-RAY DIFFRACTION5(chain A and resid 127:150)A127 - 150
6X-RAY DIFFRACTION6(chain A and resid 151:168)A151 - 168

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