[English] 日本語
Yorodumi
- PDB-6v0m: Sterile alpha-motif from apoptosis signal-regulating kinase 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v0m
TitleSterile alpha-motif from apoptosis signal-regulating kinase 3
ComponentsMitogen-activated protein kinase kinase kinase 15
KeywordsTRANSFERASE / SAM / kinase / ASK
Function / homology
Function and homology information


: / protein serine/threonine kinase activity => GO:0004674 / mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / protein kinase activity / protein serine kinase activity / ATP binding / metal ion binding
Similarity search - Function
MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / 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 ...MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / 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
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTrevelyan, S.J. / Mace, P.D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand18-UOO-152 New Zealand
CitationJournal: Sci.Signal. / Year: 2020
Title: Structure-based mechanism of preferential complex formation by apoptosis signal-regulating kinases.
Authors: Trevelyan, S.J. / Brewster, J.L. / Burgess, A.E. / Crowther, J.M. / Cadell, A.L. / Parker, B.L. / Croucher, D.R. / Dobson, R.C.J. / Murphy, J.M. / Mace, P.D.
History
DepositionNov 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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: Mitogen-activated protein kinase kinase kinase 15
B: Mitogen-activated protein kinase kinase kinase 15
C: Mitogen-activated protein kinase kinase kinase 15


Theoretical massNumber of molelcules
Total (without water)24,4873
Polymers24,4873
Non-polymers00
Water2,108117
1
A: Mitogen-activated protein kinase kinase kinase 15


Theoretical massNumber of molelcules
Total (without water)8,1621
Polymers8,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 15


Theoretical massNumber of molelcules
Total (without water)8,1621
Polymers8,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitogen-activated protein kinase kinase kinase 15


Theoretical massNumber of molelcules
Total (without water)8,1621
Polymers8,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.415, 53.558, 96.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mitogen-activated protein kinase kinase kinase 15 / Apoptosis signal-regulating kinase 3 / MAPK/ERK kinase kinase 15 / MEKK 15


Mass: 8162.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K15, ASK3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZN16, mitogen-activated protein kinase kinase kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate tribasic dihydrate pH 5, 25 % (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537, 1.456
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21.4561
ReflectionResolution: 1.8→48.13 Å / Num. obs: 22425 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.044 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.985 / Num. unique obs: 1305 / CC1/2: 0.456 / Rpim(I) all: 0.787

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→48.13 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.745 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.14
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26307 1112 5 %RANDOM
Rwork0.21927 ---
obs0.22145 21264 99.12 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 37.716 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 0 117 1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191699
X-RAY DIFFRACTIONr_bond_other_d0.0020.021652
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9282284
X-RAY DIFFRACTIONr_angle_other_deg1.2592.9383806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2635204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56723.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21615331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0531521
X-RAY DIFFRACTIONr_chiral_restr0.1080.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_mcbond_it2.6372.015825
X-RAY DIFFRACTIONr_mcbond_other2.6292.014824
X-RAY DIFFRACTIONr_mcangle_it3.3633.0031026
X-RAY DIFFRACTIONr_mcangle_other3.3653.0041027
X-RAY DIFFRACTIONr_scbond_it4.222.628874
X-RAY DIFFRACTIONr_scbond_other4.2132.629872
X-RAY DIFFRACTIONr_scangle_other6.2193.7231258
X-RAY DIFFRACTIONr_long_range_B_refined7.73525.9952102
X-RAY DIFFRACTIONr_long_range_B_other7.64325.4162072
LS refinement shellResolution: 1.8→1.843 Å
RfactorNum. reflection% reflection
Rfree0.376 70 -
Rwork0.364 1550 -
obs--98.6 %
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)
14.2788-0.3121-0.30142.533-0.20891.3540.0607-0.04210.14720.0294-0.01240.0429-0.04110.0798-0.04830.0092-0.0072-0.02550.0406-0.00920.14652.9714.62366.471
25.41051.3237-1.00942.87040.57163.18680.1263-0.35740.14170.0851-0.14380.1286-0.161-0.16930.01740.01410.0053-0.00630.0616-0.00020.181529.469-1.21777.423
33.21290.20731.26642.72490.59084.8143-0.1018-0.13360.0270.0864-0.06880.0029-0.2840.1470.17060.02690.00210.0090.10020.0140.1620.7497.20297.291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1238 - 1308
2X-RAY DIFFRACTION2B1238 - 1308
3X-RAY DIFFRACTION3C1240 - 1304

+
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