[English] 日本語
Yorodumi
- PDB-7f2x: Crystal structure of MEK1 C121S mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f2x
TitleCrystal structure of MEK1 C121S mutant
ComponentsMEK1 F11
KeywordsSIGNALING PROTEIN / Kinase
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsFujioka, Y. / Noda, N.N.
CitationJournal: Nat Commun / Year: 2022
Title: Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer.
Authors: Kubota, Y. / Fujioka, Y. / Patil, A. / Takagi, Y. / Matsubara, D. / Iijima, M. / Momose, I. / Naka, R. / Nakai, K. / Noda, N.N. / Takekawa, M.
History
DepositionJun 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MEK1 F11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2192
Polymers35,7131
Non-polymers5061
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-2 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.498, 156.504, 179.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

-
Components

#1: Protein MEK1 F11


Mass: 35713.059 Da / Num. of mol.: 1 / Mutation: C121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 3350 26%, 100 mM Bicine, 150 mM NH4F, 1% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.007→44.789 Å / Num. obs: 23080 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.198 / Net I/σ(I): 5.59
Reflection shellResolution: 2.007→2.13 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 3547 / CC1/2: 0.69 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EQC

3eqc


Resolution: 2.007→44.789 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1152 5 %
Rwork0.215 --
obs0.2159 23061 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.007→44.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 31 53 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022431
X-RAY DIFFRACTIONf_angle_d0.5833280
X-RAY DIFFRACTIONf_dihedral_angle_d14.473915
X-RAY DIFFRACTIONf_chiral_restr0.024364
X-RAY DIFFRACTIONf_plane_restr0.003417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.007-2.0980.4541350.44872594X-RAY DIFFRACTION94
2.098-2.20860.32021420.31752701X-RAY DIFFRACTION97
2.2086-2.34690.29451420.28232700X-RAY DIFFRACTION97
2.3469-2.52810.29561430.27522714X-RAY DIFFRACTION98
2.5281-2.78250.2851430.26222726X-RAY DIFFRACTION98
2.7825-3.18510.26511460.25192767X-RAY DIFFRACTION99
3.1851-4.01240.23721470.20242789X-RAY DIFFRACTION99
4.0124-44.7890.16911540.15982918X-RAY DIFFRACTION99
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)
15.5432-2.24220.43161.90920.54274.6704-0.4267-0.880.59510.28890.0962-0.9605-0.37770.33730.25890.6242-0.1177-0.08320.6459-0.2270.6007-1.087425.666433.4836
23.6398-1.4055-2.17591.68121.47023.1313-0.3914-1.21170.3340.41450.2596-0.49390.03710.2057-0.06250.54910.0501-0.10630.8478-0.1870.42235.824116.282835.014
35.3916-0.92680.62051.35421.09593.4284-0.2907-0.60220.3879-0.0010.1454-0.0728-0.24010.04720.1280.4521-0.03490.00180.3794-0.04920.4177-7.939619.811824.8518
45.9537-3.11440.00591.58620.08872.4585-0.1246-0.31790.2796-0.02970.219-0.45550.20440.5452-0.17660.3241-0.019-0.03520.4272-0.0390.4371-1.835515.197522.4025
52.8351-1.0267-1.7693.41771.03641.1619-0.3096-0.58320.5139-0.01390.0468-0.0188-0.2233-0.43470.03050.3301-0.0072-0.03350.3542-0.02180.36528.83270.675115.2568
62.8154-0.8295-0.21854.80630.20162.95450.01770.25470.0084-0.7002-0.1410.1791-0.3452-0.01360.07510.38680.0066-0.07390.3301-0.01980.2876-16.2478.87629.247
75.3575-0.9581-1.83.50243.97066.2506-0.005-0.18170.8853-0.4758-0.08090.2059-0.9035-0.25350.06640.61720.132-0.06510.4-0.02420.6378-20.719827.743419.5314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 121 )
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 221 )
5X-RAY DIFFRACTION5chain 'A' and (resid 222 through 241 )
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 321 )
7X-RAY DIFFRACTION7chain 'A' and (resid 322 through 344 )

+
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