[English] 日本語
Yorodumi
- PDB-5vyk: Crystal structure of the BRS domain of BRAF in complex with the C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vyk
TitleCrystal structure of the BRS domain of BRAF in complex with the CC-SAM domain of KSR1
ComponentsChimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf
KeywordsSIGNALING PROTEIN / BRAF / KSR1 / BRS / CC-SAM / Complex / Kinase / Pseudokinase / Signaling.
Function / homology
Function and homology information


regulation of MAP kinase activity / positive regulation of axon regeneration / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / MAP-kinase scaffold activity / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process ...regulation of MAP kinase activity / positive regulation of axon regeneration / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / MAP-kinase scaffold activity / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / myeloid progenitor cell differentiation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / negative regulation of fibroblast migration / establishment of protein localization to membrane / positive regulation of axonogenesis / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / stress fiber assembly / face development / MAP kinase kinase activity / thyroid gland development / synaptic vesicle exocytosis / somatic stem cell population maintenance / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / postsynaptic modulation of chemical synaptic transmission / negative regulation of endothelial cell apoptotic process / positive regulation of stress fiber assembly / 14-3-3 protein binding / ERK1 and ERK2 cascade / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / cellular response to calcium ion / thymus development / animal organ morphogenesis / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / centriolar satellite / ruffle membrane / cellular response to xenobiotic stimulus / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / Negative regulation of MAPK pathway / 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 / Signaling by BRAF and RAF1 fusions / T cell differentiation in thymus / T cell receptor signaling pathway / presynapse / MAPK cascade / regulation of cell population proliferation / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynapse / neuron projection / positive regulation of MAPK cascade / cilium / ciliary basal body / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / glutamatergic synapse / endoplasmic reticulum / protein-containing complex / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SAM like domain present in kinase suppressor RAS 1 / Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / : / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding ...SAM like domain present in kinase suppressor RAS 1 / Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / : / 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 / Sterile alpha motif/pointed domain superfamily / 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 / 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
Serine/threonine-protein kinase B-raf / Kinase suppressor of Ras 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.749 Å
AuthorsMaisonneuve, P. / Kurinov, I. / Marullo, S.A. / Lavoie, H. / Thevakumaran, N. / Sahmi, M. / Jin, T. / Therrien, M. / SIcheri, F.
CitationJournal: Nature / Year: 2018
Title: MEK drives BRAF activation through allosteric control of KSR proteins.
Authors: Lavoie, H. / Sahmi, M. / Maisonneuve, P. / Marullo, S.A. / Thevakumaran, N. / Jin, T. / Kurinov, I. / Sicheri, F. / Therrien, M.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf
C: Chimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3524
Polymers51,1682
Non-polymers1842
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-38 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.796, 54.336, 51.864
Angle α, β, γ (deg.)90.000, 106.680, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 56 through 161 or (resid 162...
21(chain C and ((resid 56 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLNGLN(chain A and (resid 56 through 161 or (resid 162...AA56 - 16133 - 138
12TYRTYRALAALA(chain A and (resid 56 through 161 or (resid 162...AA162 - 163139 - 140
13ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
14ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
15ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
16ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
21ARGARGARGARG(chain C and ((resid 56 and (name N or name...CB5633
22ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148
23ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148
24ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148
25ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148

-
Components

#1: Protein Chimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 25583.898 Da / Num. of mol.: 2
Fragment: UNP Q8IVT5 residues 27-172, UNP F7FV05 residues 39-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KSR1, KSR, BRAF, BRAF1, RAFB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IVT5, UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 3.0M sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.749→50 Å / Num. obs: 47556 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 40.89 Å2 / Net I/σ(I): 14.5
Reflection shellResolution: 1.749→1.85 Å / Num. unique obs: 6677 / CC1/2: 0.403 / Rrim(I) all: 2.81

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.749→49.641 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 2517 5.34 %
Rwork0.2173 44646 -
obs0.2185 47163 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.84 Å2 / Biso mean: 72.0214 Å2 / Biso min: 33.94 Å2
Refinement stepCycle: final / Resolution: 1.749→49.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 12 99 3149
Biso mean--78.95 61.08 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063114
X-RAY DIFFRACTIONf_angle_d0.754226
X-RAY DIFFRACTIONf_chiral_restr0.044502
X-RAY DIFFRACTIONf_plane_restr0.005546
X-RAY DIFFRACTIONf_dihedral_angle_d17.3651918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1040X-RAY DIFFRACTION9.359TORSIONAL
12C1040X-RAY DIFFRACTION9.359TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7494-1.78310.58811180.53112172229086
1.7831-1.81950.56081340.49182361249594
1.8195-1.8590.48161320.432471260396
1.859-1.90230.41791430.38262444258797
1.9023-1.94990.34441260.34282520264697
1.9499-2.00260.3621470.33632472261997
2.0026-2.06150.33051610.2912436259797
2.0615-2.1280.26771400.23572515265598
2.128-2.20410.29651250.21832513263898
2.2041-2.29240.22791630.21312503266699
2.2924-2.39670.22141330.21912485261899
2.3967-2.5230.25461480.22892503265198
2.523-2.68110.27671400.2312554269499
2.6811-2.88810.32631390.23512539267899
2.8881-3.17870.23291330.21912534266799
3.1787-3.63850.23721490.20212523267298
3.6385-4.58370.16441400.16822528266898
4.5837-49.66130.22131460.20762573271997
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)
14.170.06250.33735.7495-1.88647.07480.2984-0.4745-0.34330.207-0.2008-0.17380.3688-0.14830.0340.3137-0.0296-0.03390.46360.06710.29962.95230.6247.637
20.721-0.4351-0.48032.5872.78943.0084-0.2439-0.3326-0.34350.791-0.00640.011.15680.246-1.16661.4733-0.3138-0.52541.3751.54830.625663.49318.31228.56
35.06410.612.13985.4918-1.59477.32390.725-0.1219-1.73980.04960.4051-0.09921.95790.77871.50240.51970.1942-0.24920.64070.28950.695971.80224.31810.792
48.0808-1.15571.63883.3715-0.82332.0226-0.08970.5479-0.33980.19650.0625-1.10381.77980.9943-0.45640.561-0.0182-0.18011.45830.09720.763182.01827.81416.262
56.3362-1.58915.41774.8506-1.40444.7815-0.7653-0.24142.30440.19620.1985-0.1702-1.00641.08280.38040.6902-0.048-0.28581.00540.04661.244875.27336.59613.983
67.54184.0812-6.28473.9253-4.41269.94610.01880.5758-0.1251-1.00040.0594-0.29940.3633-0.1347-0.12580.6825-0.04020.03730.5236-0.0280.293357.7532.973-7.654
77.44232.7343-5.06764.432-1.54478.02890.40060.17170.2826-0.51870.15960.0279-0.1207-0.8509-0.47140.49-0.05230.05850.5022-0.01980.277651.67337.335-3.043
85.32151.3219-1.45995.6764-1.63277.460.1650.57130.8624-0.2281-0.2516-0.4364-0.63930.3671-0.10480.3011-0.02450.050.48550.15770.445366.03754.5421.415
93.24760.6805-2.38962.43771.02667.46270.4826-0.7523-0.13690.1966-0.2767-0.50980.11861.0088-0.36390.4218-0.1084-0.07281.01990.07770.809479.82552.5767.496
104.11360.5744-2.25667.3826-3.14663.50120.0623-0.31770.31441.39880.02760.3148-0.781-0.2952-0.3780.58530.03610.17410.5051-0.00880.34251.38850.03213.295
111.6051.4437-3.53171.3092-3.19497.83580.30492.05551.0249-0.3074-1.1541-1.1032-1.78560.74990.34020.74020.13610.15121.06440.32730.665450.53558.364-9.522
126.42020.777-2.01024.6765-1.57522.96660.20970.05680.07740.52540.04640.31540.6681-0.5262-0.18970.58640.00140.05850.54550.01870.274148.62543.1568.968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 33:93 )A33 - 93
2X-RAY DIFFRACTION2( CHAIN A AND RESID 94:100 )A94 - 100
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:124 )A101 - 124
4X-RAY DIFFRACTION4( CHAIN A AND RESID 125:153 )A125 - 153
5X-RAY DIFFRACTION5( CHAIN A AND RESID 154:171 )A154 - 171
6X-RAY DIFFRACTION6( CHAIN C AND RESID 1042:1068 )C1042 - 1068
7X-RAY DIFFRACTION7( CHAIN C AND RESID 1069:1105 )C1069 - 1105
8X-RAY DIFFRACTION8( CHAIN C AND RESID 33:108 )C33 - 108
9X-RAY DIFFRACTION9( CHAIN C AND RESID 109:171 )C109 - 171
10X-RAY DIFFRACTION10( CHAIN A AND RESID 1042:1068 )A1042 - 1068
11X-RAY DIFFRACTION11( CHAIN A AND RESID 1069:1075 )A1069 - 1075
12X-RAY DIFFRACTION12( CHAIN A AND RESID 1076:1104 )A1076 - 1104

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more