[English] 日本語
Yorodumi
- PDB-4dnk: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-mono... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dnk
TitleCrystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide (YWHAB) from homo sapiens at 2.20 A resolution.
Components14-3-3 protein beta/alpha
KeywordsSIGNALING 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 / protein kinase inhibitor activity / positive regulation of catalytic activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / 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 / Negative regulation of MAPK pathway / histone deacetylase binding / 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 / melanosome / Signaling by BRAF and RAF1 fusions / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide (YWHAQ) from Homo sapiens at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Structure summary
Revision 1.2Oct 21, 2015Group: Database references / Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6269
Polymers57,0932
Non-polymers5337
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-20 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.144, 122.848, 55.256
Angle α, β, γ (deg.)90.000, 113.980, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein 14-3-3 protein beta/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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS 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.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.00% polyethylene glycol 3350, 0.20M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97946,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 1, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979461
30.979321
ReflectionResolution: 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) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.263.60.7531834923200.75397.9
2.26-2.323.60.6361.2809822440.63697.5
2.32-2.393.60.5871.3801222170.58797.9
2.39-2.463.60.511.5770921280.5197.8
2.46-2.543.60.4531.7752320860.45398
2.54-2.633.60.3912733420270.39198
2.63-2.733.60.3272.4698919370.32798.1
2.73-2.843.60.2712.3666418520.27198.1
2.84-2.973.60.2093.7650017980.20998.1
2.97-3.113.60.1724.5633217420.17298.1
3.11-3.283.60.1395.5587416230.13998
3.28-3.483.60.1017.5563115570.10198.4
3.48-3.723.60.0819528214610.08198.4
3.72-4.023.60.06511.2492413600.06598.6
4.02-4.43.60.05912.4447812340.05998.2
4.4-4.923.60.05712.5406711290.05798.4
4.92-5.683.60.06510.7365810120.06598.7
5.68-6.963.60.06610.830638540.06698.7
6.96-9.843.60.04613.223736640.04698.8
9.84-29.2273.50.04314.412403560.04394.5

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1596 5.1 %RANDOM
Rwork0.192 ---
obs0.1937 31599 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 137.26 Å2 / Biso mean: 45.1948 Å2 / Biso min: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-0.23 Å2
2---1.26 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 31 257 4037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023900
X-RAY DIFFRACTIONr_bond_other_d0.0010.022693
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9735259
X-RAY DIFFRACTIONr_angle_other_deg0.81136605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4325484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73225.622201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05815759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9821523
X-RAY DIFFRACTIONr_chiral_restr0.0580.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 113 -
Rwork0.276 2154 -
all-2267 -
obs--97.88 %
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)
115.4791-15.0556-17.481414.721318.335442.9422-0.3377-0.47291.79250.28080.5172-1.62680.74062.8108-0.17950.51150.3015-0.22520.84920.07490.696740.282119.19441.187
20.8269-0.21390.5583.6723-0.67821.6594-0.0339-0.06220.0744-0.06250.10060.1635-0.0547-0.1307-0.06670.0136-0.0030.0110.06930.01380.052323.302132.51829.17
32.5592-1.34030.98586.1095-0.38292.0934-0.01580.11910.0365-0.39630.0283-0.2034-0.08150.1226-0.01250.0332-0.01510.01330.07490.01310.010824.375119.60622.405
41.45331.0185-0.89092.1533-1.16592.3863-0.03050.0507-0.0929-0.1870.0224-0.01270.11360.03450.0080.0256-0.008-0.01390.05160.01460.02489.93111.56724.399
51.8515-3.53122.627711.3215-8.010918.24920.0096-0.18620.18360.16990.20510.19-0.8839-0.6985-0.21480.06090.00720.02310.1102-0.00460.09383.103116.39932.817
61.1278-0.36210.93762.9028-0.66512.5104-0.0401-0.1131-0.03850.05550.11330.085-0.0469-0.1045-0.07320.00620.0110.01480.05840.0050.048625.443148.32736.716
72.9011-4.0906-0.467311.1477-5.185112.9512-0.1621-0.141-0.61690.6025-0.3369-0.67431.34570.18950.4990.5773-0.0973-0.3750.32210.22190.85637.975129.50150.693
81.091-0.0974-0.02875.26390.91494.61180.0002-0.0548-0.02180.1590.0801-0.33120.02290.1065-0.08030.01140.00310.00590.1456-0.02960.065932.279156.35245.39
93.6026-0.7654-0.46961.41460.35122.12220.18420.1727-0.1027-0.101-0.14110.004-0.01870.0197-0.04320.018-0.00590.00310.1021-0.03350.016919.859164.78357.955
1029.25894.12174.26736.4641-9.80119.24990.4626-1.9259-0.41140.57850.10750.3183-0.6229-0.6253-0.57010.34990.22450.17510.57330.13030.367316.391157.05170.158
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 7
2X-RAY DIFFRACTION2A8 - 90
3X-RAY DIFFRACTION3A91 - 141
4X-RAY DIFFRACTION4A142 - 210
5X-RAY DIFFRACTION5A211 - 233
6X-RAY DIFFRACTION6B1 - 72
7X-RAY DIFFRACTION7B73 - 90
8X-RAY DIFFRACTION8B91 - 141
9X-RAY DIFFRACTION9B142 - 223
10X-RAY DIFFRACTION10B224 - 234

+
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