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- PDB-7shv: Crystal structure of BRAF kinase domain bound to GDC0879 -

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Basic information

Entry
Database: PDB / ID: 7shv
TitleCrystal structure of BRAF kinase domain bound to GDC0879
ComponentsSerine/threonine-protein kinase B-raf
KeywordsTRANSFERASE/TRANSFERASE inhibitor / kinase / kinase inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / endothelial cell apoptotic process / myeloid progenitor cell differentiation / ARMS-mediated activation / negative regulation of fibroblast migration ...CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / endothelial cell apoptotic process / myeloid progenitor cell differentiation / ARMS-mediated activation / negative regulation of fibroblast migration / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / positive regulation of axonogenesis / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / face development / stress fiber assembly / thyroid gland development / MAP kinase kinase activity / somatic stem cell population maintenance / synaptic vesicle exocytosis / positive regulation of peptidyl-serine phosphorylation / negative regulation of endothelial cell apoptotic process / MAP kinase kinase kinase activity / ERK1 and ERK2 cascade / postsynaptic modulation of chemical synaptic transmission / centriolar satellite / substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / thymus development / cellular response to calcium ion / animal organ morphogenesis / sperm end piece / sperm principal piece / RAF activation / Signaling by high-kinase activity BRAF mutants / visual learning / Spry regulation of FGF signaling / MAP2K and MAPK activation / cellular response to xenobiotic stimulus / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Negative regulation of MAPK pathway / Signaling by BRAF and RAF1 fusions / T cell differentiation in thymus / MAPK cascade / T cell receptor signaling pathway / regulation of cell population proliferation / sperm midpiece / presynapse / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / protein phosphorylation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / non-specific serine/threonine protein kinase / cilium / postsynapse / ciliary basal body / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / : / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / : / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-29L / Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsKung, J.E. / Sudhamsu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Clearing the Path to Rapid High-Quality Protein Purification
Authors: Chen, X. / Wendorff, T. / Jao, C. / Kung, J.E. / Liau, N.P.D. / Wu, P. / Yu, C. / Oh, A. / Boenig, G. / Wallweber, H. / Everett, C. / Miu, A. / Brillantes, B. / Mortara, K. / Murray, J. / ...Authors: Chen, X. / Wendorff, T. / Jao, C. / Kung, J.E. / Liau, N.P.D. / Wu, P. / Yu, C. / Oh, A. / Boenig, G. / Wallweber, H. / Everett, C. / Miu, A. / Brillantes, B. / Mortara, K. / Murray, J. / Koth, C.M. / Sudhamsu, J.
History
DepositionOct 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase B-raf
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4016
Polymers70,6622
Non-polymers7404
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-16 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.638, 98.638, 159.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 35330.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-29L / 2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol


Mass: 334.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M Na Cacodylate pH 5.5, 0.1 M Ca Acetate, 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.88→39.78 Å / Num. obs: 18435 / % possible obs: 94 % / Redundancy: 13.3 % / Biso Wilson estimate: 74.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.07641 / Rrim(I) all: 0.2805 / Rsym value: 0.2696 / Net I/σ(I): 10.23
Reflection shellResolution: 2.88→3.065 Å / Redundancy: 14.1 % / Num. unique obs: 1795 / CC1/2: 0.721 / CC star: 0.915 / % possible all: 85.12

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122_finalrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MNF

4mnf


Resolution: 2.88→39.78 Å / SU ML: 0.4693 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 544 2.96 %
Rwork0.2199 17850 -
obs0.2206 18394 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.64 Å2
Refinement stepCycle: LAST / Resolution: 2.88→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 60 17 4243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01024330
X-RAY DIFFRACTIONf_angle_d1.3435846
X-RAY DIFFRACTIONf_chiral_restr0.0767643
X-RAY DIFFRACTIONf_plane_restr0.0081736
X-RAY DIFFRACTIONf_dihedral_angle_d17.30951664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.170.35381340.32574368X-RAY DIFFRACTION99.54
3.17-3.630.29891330.26294376X-RAY DIFFRACTION99.71
3.63-4.570.24831360.19734434X-RAY DIFFRACTION99.85
4.57-39.780.1921410.19474672X-RAY DIFFRACTION99.85

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