- PDB-4dnk: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-mono... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4dnk
Title
Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide (YWHAB) from homo sapiens at 2.20 A resolution.
Components
14-3-3 protein beta/alpha
Keywords
SIGNALING PROTEIN / 14-3-3 domain / phosphorylation / protein-protein binding / cell signaling / cell regulation / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information
negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling ...negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / Frs2-mediated activation / positive regulation of catalytic activity / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / histone deacetylase binding / 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 / melanosome / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function
CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
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Components
#1: Protein
14-3-3proteinbeta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1 / 14-3-3 protein beta/alpha / N- ...Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1 / 14-3-3 protein beta/alpha / N-terminally processed
Mass: 28546.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BC001359, YWHAB / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: P31946
Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 1-246 OF THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20.00% polyethylene glycol 3350, 0.20M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.2→29.227 Å / Num. all: 31601 / Num. obs: 31601 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.457 Å2 / Rsym value: 0.153 / Net I/σ(I): 7.4
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.2-2.26
3.6
0.753
1
8349
2320
0.753
97.9
2.26-2.32
3.6
0.636
1.2
8098
2244
0.636
97.5
2.32-2.39
3.6
0.587
1.3
8012
2217
0.587
97.9
2.39-2.46
3.6
0.51
1.5
7709
2128
0.51
97.8
2.46-2.54
3.6
0.453
1.7
7523
2086
0.453
98
2.54-2.63
3.6
0.391
2
7334
2027
0.391
98
2.63-2.73
3.6
0.327
2.4
6989
1937
0.327
98.1
2.73-2.84
3.6
0.271
2.3
6664
1852
0.271
98.1
2.84-2.97
3.6
0.209
3.7
6500
1798
0.209
98.1
2.97-3.11
3.6
0.172
4.5
6332
1742
0.172
98.1
3.11-3.28
3.6
0.139
5.5
5874
1623
0.139
98
3.28-3.48
3.6
0.101
7.5
5631
1557
0.101
98.4
3.48-3.72
3.6
0.081
9
5282
1461
0.081
98.4
3.72-4.02
3.6
0.065
11.2
4924
1360
0.065
98.6
4.02-4.4
3.6
0.059
12.4
4478
1234
0.059
98.2
4.4-4.92
3.6
0.057
12.5
4067
1129
0.057
98.4
4.92-5.68
3.6
0.065
10.7
3658
1012
0.065
98.7
5.68-6.96
3.6
0.066
10.8
3063
854
0.066
98.7
6.96-9.84
3.6
0.046
13.2
2373
664
0.046
98.8
9.84-29.227
3.5
0.043
14.4
1240
356
0.043
94.5
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.20
datascaling
REFMAC
5.6.0117
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.2→29.227 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.757 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.188 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 7. PHOSPHATE (PO4) MOLECULES FROM THE PURIFICATION SOLUTION ARE MODELED. 8. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2262
1596
5.1 %
RANDOM
Rwork
0.192
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obs
0.1937
31599
98.01 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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