[English] 日本語
Yorodumi
- PDB-4uy9: Structure of MLK1 kinase domain with leucine zipper 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uy9
TitleStructure of MLK1 kinase domain with leucine zipper 1
ComponentsMITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9
KeywordsTRANSFERASE / MLK FAMILY / MLK1 AND MLK3 SUBTYPE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / SH3 DOMAIN
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / MAP kinase kinase activity / protein autophosphorylation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein homodimerization activity / ATP binding
Similarity search - Function
MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsRead, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / Green, I. / Overmann, R. / Collier, M.
CitationJournal: Cancer Res. / Year: 2016
Title: Recurrent Mlk4 Loss-of-Function Mutations Suppress Jnk Signaling to Promote Colon Tumorigenesis.
Authors: Marusiak, A.A. / Stephenson, N.L. / Baik, H. / Trotter, E.W. / Li, Y. / Blyth, K. / Mason, S. / Chapman, P. / Puto, L.A. / Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / ...Authors: Marusiak, A.A. / Stephenson, N.L. / Baik, H. / Trotter, E.W. / Li, Y. / Blyth, K. / Mason, S. / Chapman, P. / Puto, L.A. / Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / Green, I. / Overman, R. / Collier, M. / Testoni, E. / Miller, C. / Hunter, T. / Sansom, O.J. / Brognard, J.
History
DepositionAug 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9
B: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9


Theoretical massNumber of molelcules
Total (without water)73,2322
Polymers73,2322
Non-polymers00
Water3,045169
1
A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9
B: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9

A: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9
B: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9


Theoretical massNumber of molelcules
Total (without water)146,4654
Polymers146,4654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6210 Å2
ΔGint-36.8 kcal/mol
Surface area51860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.930, 96.930, 416.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9 / MIXED LINEAGE KINASE 1 / MLK1 KINASE DOMAIN WITH LEUCINE ZIPP


Mass: 36616.129 Da / Num. of mol.: 2
Fragment: KINASE DOMAIN WITH N-TERMINAL LEUCINE ZIPPER 1, RESIDUES 135-456
Source method: isolated from a genetically manipulated source
Details: PROTEIN DEPHOSPHORYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P80192, mitogen-activated protein kinase kinase kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.86 Å3/Da / Density % sol: 68.17 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.8→78 Å / Num. obs: 29688 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Biso Wilson estimate: 91.25 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2
Reflection shellResolution: 2.8→3 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DTC
Resolution: 2.81→77.87 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.9212 / SU R Cruickshank DPI: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.415 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1494 5.06 %RANDOM
Rwork0.1868 ---
obs0.1889 29528 99.97 %-
Displacement parametersBiso mean: 77.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.543 Å20 Å20 Å2
2--0.543 Å20 Å2
3----1.086 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.81→77.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 0 169 4954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014917HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.26706HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1622SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes727HARMONIC5
X-RAY DIFFRACTIONt_it4917HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion21.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion654SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5395SEMIHARMONIC4
LS refinement shellResolution: 2.81→2.91 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2773 154 5.43 %
Rwork0.2289 2681 -
all0.2316 2835 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8208-1.2252-0.18132.03360.25862.35890.1307-0.05480.0256-0.2072-0.02740.1656-0.5313-0.3222-0.10330.10560.08810.0341-0.2298-0.0626-0.1921-25.519817.77049.3309
22.1715-0.1617-0.92022.20020.25233.2870.32640.0614-0.1437-0.4357-0.20410.2930.2175-0.0452-0.12230.13080.1868-0.1155-0.2899-0.0923-0.2059-57.107456.42830.0557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

+
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