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- PDB-7rjl: Crystal structure of human Bromodomain containing protein 3 (BRD3... -

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Basic information

Entry
Database: PDB / ID: 7rjl
TitleCrystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT
Components
  • Bromodomain-containing protein 3
  • Serine hydroxymethyltransferase, cytosolic
KeywordsSIGNALING PROTEIN / Brd3 / 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 / lncRNA binding / tetrahydrofolate interconversion / dTMP biosynthetic process / endodermal cell differentiation / small molecule binding / folic acid metabolic process / protein localization to chromatin / mRNA regulatory element binding translation repressor activity / molecular condensate scaffold activity / cellular response to leukemia inhibitory factor / lysine-acetylated histone binding / mRNA 5'-UTR binding / pyridoxal phosphate binding / chromatin organization / protein homotetramerization / negative regulation of translation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / 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 / NET domain superfamily / : / NET domain profile. / Brdt, bromodomain, repeat II ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / 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
Serine hydroxymethyltransferase, cytosolic / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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: Biorxiv / Year: 2021
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 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Serine hydroxymethyltransferase, cytosolic
D: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,28013
Polymers30,6914
Non-polymers5899
Water3,477193
1
A: Bromodomain-containing protein 3
C: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8109
Polymers15,3462
Non-polymers4657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-2 kcal/mol
Surface area7890 Å2
MethodPISA
2
B: Bromodomain-containing protein 3
D: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4704
Polymers15,3462
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-3 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 61.572, 83.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 14586.843 Da / Num. of mol.: 2 / Fragment: UNP residues 24-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: Q15059
#2: Protein/peptide Serine hydroxymethyltransferase, cytosolic / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 758.887 Da / Num. of mol.: 2 / Fragment: UNP residues 270-275 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P34896, glycine hydroxymethyltransferase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35% v/v Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→28.89 Å / Num. obs: 43125 / % possible obs: 99.3 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.041 / Rrim(I) all: 0.096 / Net I/σ(I): 10.9 / Num. measured all: 239500 / Scaling rejects: 204
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5350.702941318730.7080.3380.7832.387.8
8.21-28.894.80.05814983140.9930.030.0662397.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIXdev_3940refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6QJU

6qju


Resolution: 1.5→24.79 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 2161 5.02 %
Rwork0.1571 40879 -
obs0.1584 43040 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.68 Å2 / Biso mean: 26.065 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 1.5→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 149 194 2366
Biso mean--35.89 29.42 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.28271270.22262482260992
1.54-1.570.2231500.196427212871100
1.57-1.620.211670.186326772844100
1.62-1.660.22111490.184627042853100
1.66-1.720.26091310.176227052836100
1.72-1.780.18961350.167627182853100
1.78-1.850.1711370.161227182855100
1.85-1.930.17731430.158727252868100
1.93-2.040.19421360.165727412877100
2.04-2.160.17321450.147627102855100
2.16-2.330.15311710.139227252896100
2.33-2.560.17871440.147527592903100
2.56-2.940.15871470.150427562903100
2.94-3.70.1891440.15352798294299
3.7-24.790.19261350.15452940307599
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)
15.48381.66890.03013.20172.35.45-0.17360.13590.0728-0.16130.02170.28270.1014-0.17150.12620.1264-0.0230.00950.12660.05020.0871-4.0263-2.017318.7234
24.6210.862.54463.86032.10864.39720.2087-0.0079-0.22370.3754-0.0057-0.29780.54390.1899-0.21470.24630.0432-0.02110.16460.02370.134612.1488-6.75523.8506
32.0434-0.71930.29685.161-1.04191.8614-0.1841-0.47240.06720.83120.2318-0.48570.129-0.05-0.08660.22660.0393-0.08470.2424-0.03530.164314.85779.416229.9489
41.62081.0829-0.01863.25-0.04850.7228-0.0321-0.05970.08130.06870.0202-0.08460.03920.02110.01220.11190.0202-0.00950.13950.00690.11428.15087.432219.8816
55.28021.1190.94617.54451.14852.5569-0.12410.05750.0740.13110.1342-0.88210.1070.4230.00530.15710.0496-0.00460.25690.01490.258522.35875.197419.446
62.17793.392-1.8299.3682-0.34193.07440.06620.5629-0.4562-0.44670.29010.09220.2867-0.217-0.31540.320.0323-0.03380.2982-0.05910.396413.2181-11.987912.5799
75.4832-0.6046-1.53866.37952.73564.5380.3085-0.01370.5417-0.4463-0.132-0.0737-0.5318-0.07-0.16740.15810.01280.00840.1360.030.10253.341222.94341.0602
86.13812.4853-1.54733.3621-1.54592.3156-0.11560.2739-0.4403-0.26240.11320.16340.2516-0.2219-0.00560.17330.0157-0.00920.1274-0.0320.1754-1.76760.1453-2.1102
92.7028-2.9375-0.038.24241.1640.748-0.0161-0.0327-0.03640.076-0.05640.1019-0.03180.00320.05890.0838-0.00620.00770.13550.00250.0854-3.659415.25923.8326
105.6956-0.0429-1.86552.5754-0.19366.1567-0.0606-0.0165-0.4204-0.15650.0339-0.09640.26620.27590.06050.16330.01780.01950.13360.01890.15053.7005-3.08025.8408
111.22540.4358-0.68588.9993.67634.1793-0.18970.0909-0.01040.07540.1885-0.1750.1330.23710.0130.1592-0.00890.00270.17960.01910.15079.81476.34185.1693
126.5931-4.8275-2.25834.10162.97223.83960.2251-0.06060.2281-0.1537-0.0088-0.4532-0.249-0.0505-0.14710.1801-0.0267-0.00560.18410.01010.22467.741424.834210.3534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:37)A24 - 37
2X-RAY DIFFRACTION2(chain A and resid 38:53)A38 - 53
3X-RAY DIFFRACTION3(chain A and resid 54:67)A54 - 67
4X-RAY DIFFRACTION4(chain A and resid 68:116)A68 - 116
5X-RAY DIFFRACTION5(chain A and resid 117:136)A117 - 136
6X-RAY DIFFRACTION6(chain A and resid 137:143)A137 - 143
7X-RAY DIFFRACTION7(chain B and resid 32:52)B32 - 52
8X-RAY DIFFRACTION8(chain B and resid 53:78)B53 - 78
9X-RAY DIFFRACTION9(chain B and resid 79:109)B79 - 109
10X-RAY DIFFRACTION10(chain B and resid 110:121)B110 - 121
11X-RAY DIFFRACTION11(chain B and resid 122:134)B122 - 134
12X-RAY DIFFRACTION12(chain B and resid 135:144)B135 - 144

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