[English] 日本語
Yorodumi
- PDB-5k26: Structure of the SH3 domain of MLK3 bound to peptide generated fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k26
TitleStructure of the SH3 domain of MLK3 bound to peptide generated from phage display
ComponentsMitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP
KeywordsTRANSFERASE / MLK3 / SH3 / phage display / signalling protein
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / RHOV GTPase cycle / positive regulation of JUN kinase activity / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity ...mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / RHOV GTPase cycle / positive regulation of JUN kinase activity / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity / microtubule-based process / JNK cascade / positive regulation of JNK cascade / RAF activation / small GTPase binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of neuron apoptotic process / MAPK cascade / protein autophosphorylation / microtubule / protein phosphorylation / protein kinase activity / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein homodimerization activity / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKall, S.K. / Lavie, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification of two distinct peptide-binding pockets in the SH3 domain of human mixed-lineage kinase 3.
Authors: Kokoszka, M.E. / Kall, S.L. / Khosla, S. / McGinnis, J.E. / Lavie, A. / Kay, B.K.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP
B: Mitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9183
Polymers18,7222
Non-polymers1951
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 64.000, 35.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Mitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP / Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase


Mass: 9361.192 Da / Num. of mol.: 2
Fragment: SH3 domain (UNP residues 41-105),SH3 domain (UNP residues 41-105)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K11, MLK3, PTK1, SPRK / Production host: Escherichia coli (E. coli)
References: UniProt: Q16584, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.31 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na-Phosphate, 0.1 M K-Phosphate, 0.1 M MES 6.5, 1.5 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→55.43 Å / Num. obs: 48242 / % possible obs: 97.2 % / Redundancy: 4.92 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.53
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.76 / % possible all: 83.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SEM

1sem


Resolution: 1.2→55.43 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.764 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16826 2412 4.9 %RANDOM
Rwork0.13712 ---
obs0.13865 46672 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.2→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 12 123 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0191292
X-RAY DIFFRACTIONr_bond_other_d0.0050.021171
X-RAY DIFFRACTIONr_angle_refined_deg3.0061.9281769
X-RAY DIFFRACTIONr_angle_other_deg1.58532685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60623.23568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76415186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0481515
X-RAY DIFFRACTIONr_chiral_restr0.1780.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211571
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02336
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4751.675646
X-RAY DIFFRACTIONr_mcbond_other3.4591.666645
X-RAY DIFFRACTIONr_mcangle_it4.3082.513813
X-RAY DIFFRACTIONr_mcangle_other4.3262.518814
X-RAY DIFFRACTIONr_scbond_it7.92.172646
X-RAY DIFFRACTIONr_scbond_other7.9012.171646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.0043.101951
X-RAY DIFFRACTIONr_long_range_B_refined9.8515.2111429
X-RAY DIFFRACTIONr_long_range_B_other9.84715.2221430
X-RAY DIFFRACTIONr_rigid_bond_restr7.21432463
X-RAY DIFFRACTIONr_sphericity_free32.597544
X-RAY DIFFRACTIONr_sphericity_bonded21.6252502
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 115 -
Rwork0.278 2666 -
obs--73.92 %

+
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