[English] 日本語
Yorodumi
- PDB-6mcq: L. pneumophila effector kinase LegK7 in complex with human MOB1A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mcq
TitleL. pneumophila effector kinase LegK7 in complex with human MOB1A
Components
  • LegK7
  • MOB kinase activator 1A
KeywordsTRANSFERASE / translocated effector / Ser/Thr protein kinase / allosteric activation / Hippo pathway
Function / homology
Function and homology information


hippo signaling / Signaling by Hippo / protein kinase activator activity / positive regulation of protein phosphorylation / extracellular exosome / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein kinase domain containing protein / MOB kinase activator 1A
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsBeyrakhova, K.A. / Xu, C. / Boniecki, M.T. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-48370 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: TheLegionellakinase LegK7 exploits the Hippo pathway scaffold protein MOB1A for allostery and substrate phosphorylation.
Authors: Lee, P.C. / Beyrakhova, K. / Xu, C. / Boniecki, M.T. / Lee, M.H. / Onu, C.J. / Grishin, A.M. / Machner, M.P. / Cygler, M.
History
DepositionSep 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 11, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Jun 10, 2020Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LegK7
B: MOB kinase activator 1A
C: LegK7
D: MOB kinase activator 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,35530
Polymers164,7084
Non-polymers3,64726
Water2,090116
1
A: LegK7
B: MOB kinase activator 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91019
Polymers82,3542
Non-polymers2,55617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LegK7
D: MOB kinase activator 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,44411
Polymers82,3542
Non-polymers1,0919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.400, 113.100, 157.850
Angle α, β, γ (deg.)90.000, 106.000, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein LegK7


Mass: 60684.215 Da / Num. of mol.: 2 / Fragment: UNP residues 11-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1924 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5ZU83, non-specific serine/threonine protein kinase
#2: Protein MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


Mass: 21669.703 Da / Num. of mol.: 2 / Fragment: UNP residues 33-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H8S9

-
Non-polymers , 5 types, 142 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 23% PEG600, 0.1 M lithium chloride, 20 mM succinate, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.57→49.493 Å / Num. obs: 57771 / % possible obs: 99.8 % / Redundancy: 5.058 % / Biso Wilson estimate: 58.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.115 / Χ2: 0.998 / Net I/σ(I): 9.72 / Num. measured all: 292177 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.57-2.644.930.8741.8220942425542480.7480.9899.8
2.64-2.715.280.7332.3121990417241650.810.81599.8
2.71-2.795.2860.5812.9521399405340480.8720.64699.9
2.79-2.875.2370.4943.4820336387938830.9050.55100
2.87-2.975.1930.4224.0219750380938030.9320.4799.8
2.97-3.075.0560.3464.7118665369236920.9450.386100
3.07-3.194.8740.2675.7117196353235280.9620.399.9
3.19-3.325.2040.217.5417808342634220.9780.23499.9
3.32-3.474.8670.1668.815969329232810.9840.18699.7
3.47-3.635.1890.12411.3616336315431480.9920.13899.8
3.63-3.835.1720.09913.3615413297829800.9940.11100
3.83-4.065.0140.08215.8814244284828410.9960.09299.8
4.06-4.344.8670.0717.0812975267926660.9960.07899.5
4.34-4.694.6670.06218.3611332243624280.9960.0799.7
4.69-5.144.8240.05919.2611124230723060.9970.066100
5.14-5.755.0150.05819.0410316206020570.9980.06599.9
5.75-6.645.180.05919.199510183918360.9970.06699.8
6.64-8.134.8710.04921.187618156715640.9980.05599.8
8.13-11.494.8210.03725.255795120712020.9980.04299.6
11.49-49.4935.140.0427.1534596876730.9980.04598

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.57→49.493 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 2884 5 %
Rwork0.1985 54831 -
obs0.2009 57715 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.59 Å2 / Biso mean: 72.2474 Å2 / Biso min: 28.77 Å2
Refinement stepCycle: final / Resolution: 2.57→49.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11120 0 230 116 11466
Biso mean--88.12 59.08 -
Num. residues----1403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311619
X-RAY DIFFRACTIONf_angle_d0.56415693
X-RAY DIFFRACTIONf_chiral_restr0.041726
X-RAY DIFFRACTIONf_plane_restr0.0052029
X-RAY DIFFRACTIONf_dihedral_angle_d16.3146980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.57-2.61210.32991360.287926022738100
2.6121-2.65710.35471370.294225962733100
2.6571-2.70540.34341370.281525972734100
2.7054-2.75750.31931370.278725892726100
2.7575-2.81380.33041360.271326122748100
2.8138-2.87490.28781360.262425812717100
2.8749-2.94180.31171370.25825992736100
2.9418-3.01540.29391380.235426182756100
3.0154-3.09690.27481360.241225922728100
3.0969-3.1880.2521360.237925862722100
3.188-3.29090.28051380.236126302768100
3.2909-3.40850.28181380.24126202758100
3.4085-3.54490.30151370.220825972734100
3.5449-3.70620.27791380.20626292767100
3.7062-3.90150.23721370.188126022739100
3.9015-4.14580.20621380.172626162754100
4.1458-4.46570.18981360.153825942730100
4.4657-4.91480.21041390.152826362775100
4.9148-5.62510.19721380.168726272765100
5.6251-7.08370.27761400.197926522792100
7.0837-49.50210.1821390.15712656279599
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)
17.65010.89690.93484.35261.31183.1533-0.10910.014-0.0169-0.16830.1584-0.1825-0.28190.2991-0.01010.4087-0.1036-0.0210.3813-0.00320.2925100.316756.003354.3482
23.3707-0.20021.12760.9314-0.48533.1202-0.07770.14820.1671-0.1437-0.07570.1101-0.1591-0.15030.13150.4332-0.0123-0.03770.3176-0.03210.348884.660952.983150.4458
31.44640.1237-0.12172.51380.2551.9862-0.0177-0.0770.0552-0.11420.10390.2887-0.1696-0.1794-0.0780.3227-0.01150.00990.2970.03240.307758.99254.779664.7358
49.29611.136-2.69510.28850.23943.02510.4559-0.23750.26820.5812-0.091.5920.0624-1.0015-0.42210.65880.06960.15461.0191-0.05521.223536.862953.57283.2764
52.65331.4687-0.62463.00550.32782.4873-0.06380.1088-0.1541-0.08310.2056-0.02790.1387-0.0361-0.15620.3765-0.0476-0.03210.27220.03810.420363.346624.981461.9801
65.8243-2.0676-0.57245.07550.16663.8482-0.0537-0.21670.0024-0.01290.34110.6297-0.063-0.5303-0.28370.39320.0571-0.05460.61070.09190.551639.804460.664219.0497
75.12011.38571.37013.2361.18474.6418-0.0034-0.49730.14220.1560.0352-0.0215-0.3964-0.2777-0.04330.41220.14640.04280.47520.06850.390656.799958.887528.3974
82.9164-0.554-0.38512.0986-0.14641.65690.07590.35440.3005-0.1092-0.0148-0.441-0.22630.4012-0.06920.4372-0.0130.0060.5514-0.01770.516383.430559.96958.1909
94.7826-1.3114-1.45072.4986-0.43282.5353-0.2749-0.2665-0.51930.08320.26230.01590.2690.02180.00870.50680.077-0.0090.4063-0.05090.645376.083130.51314.2886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 104 )A10 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 262 )A105 - 262
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 479 )A263 - 479
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 528 )A480 - 528
5X-RAY DIFFRACTION5chain 'B'B31 - 213
6X-RAY DIFFRACTION6chain 'C' and (resid 11 through 130 )C11 - 130
7X-RAY DIFFRACTION7chain 'C' and (resid 131 through 258 )C131 - 258
8X-RAY DIFFRACTION8chain 'C' and (resid 259 through 529 )C259 - 529
9X-RAY DIFFRACTION9chain 'D'D32 - 213

+
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