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- PDB-8x7h: Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-B... -

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Basic information

Entry
Database: PDB / ID: 8x7h
TitleCrystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).
Components
  • Bromodomain-containing protein 4
  • Glucose-induced degradation protein 4 homolog
KeywordsCYTOSOLIC PROTEIN / ubiquitin ligase
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / negative regulation by host of viral transcription / ubiquitin ligase complex / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / Regulation of pyruvate metabolism / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / negative regulation by host of viral transcription / ubiquitin ligase complex / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / Regulation of pyruvate metabolism / condensed nuclear chromosome / histone reader activity / : / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / p53 binding / ubiquitin protein ligase activity / chromosome / regulation of inflammatory response / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain ...Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 4 / Glucose-induced degradation protein 4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDong, C. / Yan, X. / Li, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32271265 China
National Natural Science Foundation of China (NSFC)32071193 China
CitationJournal: To Be Published
Title: Crystal structure of 162
Authors: Dong, C. / Yan, X. / Li, Y.
History
DepositionNov 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-induced degradation protein 4 homolog
B: Bromodomain-containing protein 4
C: Glucose-induced degradation protein 4 homolog
D: Bromodomain-containing protein 4
E: Glucose-induced degradation protein 4 homolog
F: Bromodomain-containing protein 4
G: Glucose-induced degradation protein 4 homolog
H: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,61520
Polymers138,1728
Non-polymers4,44312
Water1,15364
1
A: Glucose-induced degradation protein 4 homolog
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5624
Polymers34,5432
Non-polymers1,0192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glucose-induced degradation protein 4 homolog
D: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8387
Polymers34,5432
Non-polymers1,2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glucose-induced degradation protein 4 homolog
F: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4703
Polymers34,5432
Non-polymers9271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Glucose-induced degradation protein 4 homolog
H: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7466
Polymers34,5432
Non-polymers1,2034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.855, 87.613, 88.440
Angle α, β, γ (deg.)103.09, 90.90, 106.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog


Mass: 19604.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7
#2: Protein
Bromodomain-containing protein 4 / Protein HUNK1


Mass: 14938.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#3: Chemical
ChemComp-YBI / ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide


Mass: 926.570 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C50H56ClN11O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.9→47.81 Å / Num. obs: 34488 / % possible obs: 97.07 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.97
Reflection shellResolution: 2.9→3.01 Å / Rmerge(I) obs: 0.528 / Num. unique obs: 3438

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→38.46 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 38.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.301 1713 5.02 %
Rwork0.2355 --
obs0.2388 34141 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8030 0 317 64 8411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148625
X-RAY DIFFRACTIONf_angle_d1.7591179
X-RAY DIFFRACTIONf_dihedral_angle_d13.3311241
X-RAY DIFFRACTIONf_chiral_restr0.0781198
X-RAY DIFFRACTIONf_plane_restr0.0171509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.43661490.37912727X-RAY DIFFRACTION96
2.99-3.080.36161380.31722671X-RAY DIFFRACTION98
3.09-3.20.41131450.30672732X-RAY DIFFRACTION98
3.2-3.320.39031440.30792725X-RAY DIFFRACTION97
3.32-3.470.35831440.28052685X-RAY DIFFRACTION97
3.47-3.660.33091430.23892735X-RAY DIFFRACTION98
3.66-3.890.29591380.21922667X-RAY DIFFRACTION97
3.89-4.190.26651470.20132707X-RAY DIFFRACTION97
4.19-4.610.21761360.18882736X-RAY DIFFRACTION98
4.61-5.270.22711410.19452720X-RAY DIFFRACTION98
5.27-6.630.32221480.24132687X-RAY DIFFRACTION97
6.64-38.460.28811400.21612636X-RAY DIFFRACTION95

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