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- PDB-3ny5: Crystal structure of the RBD domain of serine/threonine-protein k... -

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Basic information

Entry
Database: PDB / ID: 3ny5
TitleCrystal structure of the RBD domain of serine/threonine-protein kinase B-raf from Homo sapiens. Northeast Structural Genomics Consortium Target HR4694F
ComponentsSerine/threonine-protein kinase B-raf
KeywordsTRANSFERASE / NESG / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.993 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the RBD domain of serine/threonine-protein kinase B-raf from Homo sapiens.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,0464
Polymers45,0464
Non-polymers00
Water4,504250
1
A: Serine/threonine-protein kinase B-raf
B: Serine/threonine-protein kinase B-raf


Theoretical massNumber of molelcules
Total (without water)22,5232
Polymers22,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area9950 Å2
MethodPISA
2
C: Serine/threonine-protein kinase B-raf

D: Serine/threonine-protein kinase B-raf


Theoretical massNumber of molelcules
Total (without water)22,5232
Polymers22,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y+1/2,-z+3/21
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area9620 Å2
MethodPISA
3
C: Serine/threonine-protein kinase B-raf
D: Serine/threonine-protein kinase B-raf


Theoretical massNumber of molelcules
Total (without water)22,5232
Polymers22,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.805, 69.418, 114.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDimer according to aggregation screening

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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: 11261.486 Da / Num. of mol.: 4 / Fragment: RBD domain residues 153-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 6.5
Details: 28% PEG 2000, 0.1M Bis-tris, pH 6.5, Microbatch under Paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 41777 / Num. obs: 41610 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 38.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 9.1 / Num. unique all: 4119 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.993→37.602 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.23 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2132 5.14 %RANDOM
Rwork0.21 ---
obs0.213 41488 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.594 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 132.85 Å2 / Biso mean: 31.144 Å2 / Biso min: 5.26 Å2
Baniso -1Baniso -2Baniso -3
1--6.197 Å2-0 Å20 Å2
2---3.228 Å20 Å2
3---9.425 Å2
Refinement stepCycle: LAST / Resolution: 1.993→37.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 0 250 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152629
X-RAY DIFFRACTIONf_angle_d1.5213569
X-RAY DIFFRACTIONf_chiral_restr0.104423
X-RAY DIFFRACTIONf_plane_restr0.007446
X-RAY DIFFRACTIONf_dihedral_angle_d15.3161007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.993-2.0390.251280.1872422255093
2.039-2.090.2451500.19526912841100
2.09-2.1470.2831210.20226252746100
2.147-2.210.2951550.18626522807100
2.21-2.2810.2321330.20226222755100
2.281-2.3630.2821260.19226852811100
2.363-2.4570.2751440.21326352779100
2.457-2.5690.2861560.20726352791100
2.569-2.7050.2891690.21326062775100
2.705-2.8740.291360.21126612797100
2.874-3.0960.2531510.20426482799100
3.096-3.4070.2731670.18526052772100
3.407-3.90.2361260.18326712797100
3.9-4.9120.2311430.1826242767100
4.912-37.6080.2831270.2542574270196
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)
11.4972-0.17650.23850.9762-0.12840.6417-0.0036-00.0470.00050.00020.0856-0.08050.02680.00140.07710.00030.01270.04820.00240.03552.555444.496960.2131
20.9312-0.414-0.03970.87240.16760.62260.0064-0.0007-0.11250.01830.0019-0.07180.0352-0.0401-0.01820.0584-0.0113-0.02140.0574-0.00310.061914.914225.188960.1907
31.75950.49280.08260.8146-0.08081.0578-0.01670.07180.20710.0064-0.03890.32860.0525-0.02260.04630.0562-0.0104-0.01010.0874-0.01530.12254.381663.658482.4547
41.4777-0.33330.16040.816-0.04920.6911-0.068-0.0073-0.0460.0594-0.02990.1502-0.06020.07270.07840.0870.00290.01210.1081-0.01130.08423.85348.141688.5362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA151 - 233
2X-RAY DIFFRACTION2chain BB150 - 235
3X-RAY DIFFRACTION3chain CC152 - 235
4X-RAY DIFFRACTION4chain DD151 - 232

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