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- PDB-4wo5: Crystal structure of a BRAF kinase domain monomer -

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Basic information

Entry
Database: PDB / ID: 4wo5
TitleCrystal structure of a BRAF kinase domain monomer
ComponentsSerine/threonine-protein kinase B-raf
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Kinase / Monomer / Inhibitor / Complex / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


trehalose metabolism in response to stress / Signaling by MRAS-complex mutants / Signalling to p38 via RIT and RIN / positive regulation of glucose transmembrane transport / ARMS-mediated activation / establishment of protein localization to membrane / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / MAP kinase kinase activity / cellular response to calcium ion ...trehalose metabolism in response to stress / Signaling by MRAS-complex mutants / Signalling to p38 via RIT and RIN / positive regulation of glucose transmembrane transport / ARMS-mediated activation / establishment of protein localization to membrane / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / MAP kinase kinase activity / cellular response to calcium ion / RAF activation / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / animal organ morphogenesis / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / Negative regulation of MAPK pathway / MAPK cascade / Signaling by RAF1 mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by moderate kinase activity BRAF mutants / Signaling by BRAF and RAF1 fusions / scaffold protein binding / positive regulation of peptidyl-serine phosphorylation / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / protein kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity => GO:0004674 / protein phosphorylation / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding domain / Ras-binding domain (RBD) profile. / Raf-like Ras-binding / 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 ...Raf-like Ras-binding domain / Raf-like Ras-binding domain / Ras-binding domain (RBD) profile. / Raf-like Ras-binding / 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 / Ubiquitin-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinases ATP-binding region signature. / Protein kinase, ATP binding site / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-324 / Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsCritton, D.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation.
Authors: Thevakumaran, N. / Lavoie, H. / Critton, D.A. / Tebben, A. / Marinier, A. / Sicheri, F. / Therrien, M.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations

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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)69,0614
Polymers68,2342
Non-polymers8282
Water1,38777
1
A: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5312
Polymers34,1171
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5312
Polymers34,1171
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)65.610, 72.748, 243.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-906-

HOH

21B-902-

HOH

31B-907-

HOH

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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: 34116.914 Da / Num. of mol.: 2 / Fragment: UNP residues 444-723
Mutation: I543A, I544S, I551K, Q562R, L588N, K630S, F667E, Y673S, A688R, L706S, Q709R, S713E, L716E, S720E, P722S, K723G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha]
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-324 / N-{3-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-difluorophenyl}propane-1-sulfonamide


Mass: 413.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14ClF2N3O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M trimethylamine-N-oxide, 20% (w/v) PEG-MME 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→38.03 Å / Num. obs: 14335 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 79.47 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.2
Reflection shellResolution: 2.83→2.99 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4C
Resolution: 2.83→38.03 Å / Cor.coef. Fo:Fc: 0.9292 / Cor.coef. Fo:Fc free: 0.8742 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 720 5.02 %RANDOM
Rwork0.1929 ---
obs0.1961 14335 99.79 %-
Displacement parametersBiso mean: 57.27 Å2
Baniso -1Baniso -2Baniso -3
1-5.5227 Å20 Å20 Å2
2---8.9099 Å20 Å2
3---3.3872 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: 1 / Resolution: 2.83→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 54 77 4109
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094121HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.195599HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1390SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes605HARMONIC5
X-RAY DIFFRACTIONt_it4121HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion21.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion547SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4815SEMIHARMONIC4
LS refinement shellResolution: 2.83→3.06 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3122 166 5.77 %
Rwork0.2196 2710 -
all0.2251 2876 -
obs--99.79 %

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