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- PDB-4jvg: B-Raf Kinase in Complex with Birb796 -

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Basic information

Entry
Database: PDB / ID: 4jvg
TitleB-Raf Kinase in Complex with Birb796
ComponentsSerine/threonine-protein kinase B-raf
KeywordsTransferase/transferase inhibitor / kinase / phosphotransferase / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / negative regulation of fibroblast migration / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / positive regulation of axonogenesis / regulation of T cell differentiation / mitogen-activated protein kinase kinase binding / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / positive regulation of axon regeneration / stress fiber assembly / face development / MAP kinase kinase activity / synaptic vesicle exocytosis / thyroid gland development / somatic stem cell population maintenance / MAP kinase kinase kinase activity / postsynaptic modulation of chemical synaptic transmission / negative regulation of endothelial cell apoptotic process / response to cAMP / positive regulation of peptidyl-serine phosphorylation / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / ERK1 and ERK2 cascade / substrate adhesion-dependent cell spreading / cellular response to calcium ion / thymus development / animal organ morphogenesis / RAF activation / cellular response to nerve growth factor stimulus / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / response to peptide hormone / centriolar satellite / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / MAPK cascade / cellular response to xenobiotic stimulus / presynapse / T cell receptor signaling pathway / regulation of cell population proliferation / T cell differentiation in thymus / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / postsynapse / protein kinase activity / neuron projection / ciliary basal body / cilium / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / glutamatergic synapse / mitochondrion / zinc ion binding
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-B96 / Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsLavoie, H. / Thevakumaran, N. / Gavory, G. / Li, J. / Padeganeh, A. / Guiral, S. / Duchaine, J. / Mao, D.Y.L. / Bouvier, M. / Sicheri, F. / Therrien, M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization.
Authors: Lavoie, H. / Thevakumaran, N. / Gavory, G. / Li, J.J. / Padeganeh, A. / Guiral, S. / Duchaine, J. / Mao, D.Y. / Bouvier, M. / Sicheri, F. / Therrien, M.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,1108
Polymers129,0004
Non-polymers2,1114
Water00
1
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7782
Polymers32,2501
Non-polymers5281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7782
Polymers32,2501
Non-polymers5281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7782
Polymers32,2501
Non-polymers5281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7782
Polymers32,2501
Non-polymers5281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.997, 120.610, 81.714
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211

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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: 32249.941 Da / Num. of mol.: 4 / Fragment: Kinase Domain
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 / Production host: Escherichia coli (E. coli)
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-B96 / 1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA


Mass: 527.657 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H37N5O3

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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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M BisTris propane, 30% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012
RadiationMonochromator: Kohu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. all: 17464 / Num. obs: 17464 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rsym value: 0.104
Reflection shellResolution: 3.09→3.17 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1 / Rsym value: 0.538 / % possible all: 92.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→42.541 Å / SU ML: 0.79 / σ(F): 1.39 / Phase error: 42.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.295 893 5.11 %
Rwork0.2316 --
obs0.2349 17464 89.5 %
all-17464 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.341 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.031 Å2-0 Å2-3.3163 Å2
2---4.6475 Å2-0 Å2
3---0.6165 Å2
Refinement stepCycle: LAST / Resolution: 3.09→42.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 156 0 8481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088665
X-RAY DIFFRACTIONf_angle_d1.4211688
X-RAY DIFFRACTIONf_dihedral_angle_d17.4513296
X-RAY DIFFRACTIONf_chiral_restr0.0921258
X-RAY DIFFRACTIONf_plane_restr0.0091481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.28760.40961380.37712773X-RAY DIFFRACTION91
3.2876-3.54130.34851470.30242684X-RAY DIFFRACTION87
3.5413-3.89740.32021480.25982914X-RAY DIFFRACTION94
3.8974-4.46090.27471600.19782777X-RAY DIFFRACTION91
4.4609-5.61820.25371500.19172854X-RAY DIFFRACTION92
5.6182-42.54460.26781500.18672569X-RAY DIFFRACTION82
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)
11.7486-0.16660.52691.5850.03490.5338-0.4078-0.43870.18430.62330.2067-0.3177-0.29430.1576-0.05150.620.1091-0.6493-0.17440.38850.086915.7312-0.848251.8828
21.59010.2373-0.21080.4704-0.36660.30160.1531-0.27520.53220.26350.23940.01550.03430.16630.78750.8490.5413-0.13390.4864-0.63730.4387.6435-0.104551.6876
30.77990.1466-0.16060.7240.08542.26980.2389-0.3830.29770.1145-0.0149-0.0761-0.52690.56020.36410.1517-0.1928-0.2484-0.2534-0.833-0.517713.25913.268634.4689
41.72091.5739-0.35132.0247-0.29320.88030.2110.17940.9073-0.08710.11990.9066-0.6851-0.1382-0.2486-0.2429-0.98740.1548-2.33220.1481-0.13863.776811.203833.5358
50.3482-0.69710.03931.3783-0.10390.66850.1099-0.04780.62560.18120.22060.111-0.5227-0.0638-0.1140.877-0.0450.01580.0971-0.00230.79253.053327.995731.9235
61.67330.2679-0.77032.58650.16621.53720.27530.2955-0.144-0.5040.46470.0556-0.1331-0.07180.04270.42940.0153-0.27490.1143-0.1905-0.55693.064112.328718.2933
70.79860.4913-0.56881.7445-0.8592.8595-0.21590.5776-0.2178-0.06310.02880.24750.3736-0.32190.20240.58630.15850.03790.7978-0.21070.255.7627-16.433724.2258
81.5480.6684-0.64630.7827-0.95411.1373-0.3940.1089-0.8275-0.38640.14610.21620.8094-0.5677-0.10020.1334-0.4513-0.0896-0.40180.23620.87016.6066-21.344231.5624
91.7151-0.17190.43550.79850.4421.3043-0.051-0.3077-0.7764-0.20680.4762-0.34840.09830.53850.86090.0477-0.3470.28210.30930.47960.304224.5168-20.997734.597
101.8394-0.2968-0.20234.4202-0.27912.8785-0.1472-0.0969-0.4094-0.26660.4111-1.04790.16760.19460.2555-0.2631-0.6384-0.5133-0.892-0.15830.539436.5597-25.105940.9251
111.27990.33020.88271.54730.57591.84760.0376-0.2189-0.02660.11940.17760.0159-0.0463-0.10140.32240.75640.2464-0.44891.0992-0.15960.12842.9236-0.828392.7418
123.75720.17890.30921.6963-0.22562.6515-0.4184-0.6040.32220.61820.21690.4586-0.7437-0.8672-0.48840.43440.1827-0.0090.45990.24950.340834.8116-0.075492.4804
131.9578-0.27210.35771.41830.09010.8417-0.1548-0.1520.10320.2039-0.0436-0.1615-0.5040.22690.40911.06320.2248-0.52510.21640.43550.545142.59953.498879.8987
140.53120.3148-0.30750.4358-0.4061.31530.12280.12740.243-0.05510.34590.6826-0.4949-0.4612-0.22110.47340.6732-0.97-0.25691.1118-0.078932.5098.104373.3942
150.790.36410.00311.3899-0.53080.90450.23960.01780.3952-0.09670.28040.4612-0.546-0.19510.17241.01580.6021-0.6888-0.20140.7943-0.034330.398915.947763.8513
160.5093-0.393-0.25381.25510.38471.143-0.17150.1688-0.0485-0.07290.07850.0950.20530.1885-0.52070.6522-0.0525-0.8402-0.5702-0.19420.117132.9836-16.40365.0663
173.86152.3943-2.00456.3896-1.70982.6761-0.23870.646-0.85-1.5397-0.0961.15771.0686-0.24840.09221.3020.1933-0.21510.6297-0.34370.899232.0156-25.627165.523
180.1767-0.4163-0.41361.22320.80210.9696-0.17720.2598-0.2958-0.2046-0.34490.60680.3551-0.3619-0.76870.3420.5866-0.2566-0.726-0.7659-0.48342.6948-17.84371.484
191.779-0.92920.09550.70080.37860.94580.07070.0054-0.63260.21320.13320.28610.6743-0.0256-0.08460.01941.3675-0.591-0.89430.01320.318651.2817-22.79378.5946
201.3572-1.0152-0.30741.00770.2090.3803-0.1198-0.2627-0.34240.09740.4018-0.63160.28620.50190.3143-0.01861.2718-0.10330.1964-0.40160.763663.7366-25.13581.7854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 448:475)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 476:507)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 508:570)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 571:651)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 652:671)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 672:722)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 448:478)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 479:524)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 525:634)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 635:722)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 448:475)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 476:507)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 508:549)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 550:634)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 635:722)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 448:478)
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 479:493)
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 494:549)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 550:634)
20X-RAY DIFFRACTION20CHAIN D AND (RESSEQ 635:722)

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