[English] 日本語
Yorodumi
- PDB-6una: Crystal structure of inactive p38gamma -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6una
TitleCrystal structure of inactive p38gamma
ComponentsMitogen-activated protein kinase 12
KeywordsTRANSFERASE / MAPK / mitogen activated protein kinase / p38 gamma / MAPK12 / inactive kinase
Function / homology
Function and homology information


positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / positive regulation of muscle cell differentiation / muscle organ development / Myogenesis / negative regulation of cell cycle / MAP kinase activity / signal transduction in response to DNA damage / JUN kinase activity ...positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / positive regulation of muscle cell differentiation / muscle organ development / Myogenesis / negative regulation of cell cycle / MAP kinase activity / signal transduction in response to DNA damage / JUN kinase activity / mitogen-activated protein kinase / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / Negative regulation of MAPK pathway / MAPK cascade / peptidyl-serine phosphorylation / regulation of cell cycle / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 12 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Mitogen-activated protein kinase 12 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitogen-activated protein kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.554 Å
AuthorsAoto, P.C. / Stanfield, R.L. / Wilson, I.A. / Dyson, H.J. / Wright, P.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM75995 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Biochemistry / Year: 2019
Title: A Dynamic Switch in Inactive p38 gamma Leads to an Excited State on the Pathway to an Active Kinase.
Authors: Aoto, P.C. / Stanfield, R.L. / Wilson, I.A. / Dyson, H.J. / Wright, P.E.
History
DepositionOct 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 12
B: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2356
Polymers82,8592
Non-polymers3764
Water81145
1
A: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6183
Polymers41,4301
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6183
Polymers41,4301
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.032, 66.359, 68.568
Angle α, β, γ (deg.)115.270, 102.490, 96.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 69 or resid 71...
21(chain B and (resid 10 through 69 or resid 71...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS(chain A and (resid 10 through 69 or resid 71...AA10 - 694 - 63
12ALAALALEULEU(chain A and (resid 10 through 69 or resid 71...AA71 - 17065 - 164
13PHEPHEGLYGLY(chain A and (resid 10 through 69 or resid 71...AA172 - 173166 - 167
14GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
15GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
16GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
17GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
18GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
19GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
21GLYGLYLYSLYS(chain B and (resid 10 through 69 or resid 71...BB10 - 694 - 63
22ALAALALEULEU(chain B and (resid 10 through 69 or resid 71...BB71 - 17065 - 164
23PHEPHEGLUGLU(chain B and (resid 10 through 69 or resid 71...BB172 - 318166 - 312
24PROPROPHEPHE(chain B and (resid 10 through 69 or resid 71...BB321 - 351315 - 345

-
Components

#1: Protein Mitogen-activated protein kinase 12 / MAPK 12 / Extracellular signal-regulated kinase 6 / ERK-6 / Mitogen-activated protein kinase p38 ...MAPK 12 / Extracellular signal-regulated kinase 6 / ERK-6 / Mitogen-activated protein kinase p38 gamma / MAP kinase p38 gamma / Stress-activated protein kinase 3


Mass: 41429.500 Da / Num. of mol.: 2 / Mutation: Q31R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK12, ERK6, SAPK3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P53778, mitogen-activated protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.7 / Details: 2.4M Ammonium sulfate, 50mM TRIS pH 7.7.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.55→44.585 Å / Num. obs: 22388 / % possible obs: 98.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 42.33 Å2 / CC1/2: 0.91 / Rpim(I) all: 0.075 / Rrim(I) all: 0.11 / Rsym value: 0.075 / Net I/σ(I): 10.3
Reflection shellResolution: 2.55→2.62 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1051 / CC1/2: 0.68 / Rpim(I) all: 0.37 / Rrim(I) all: 0.53 / Rsym value: 0.37

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cm8

1cm8


Resolution: 2.554→44.585 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2455 1112 4.97 %
Rwork0.1953 --
obs0.1978 22386 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.81 Å2 / Biso mean: 50.366 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 2.554→44.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 22 45 5406
Biso mean--76.42 38.19 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035488
X-RAY DIFFRACTIONf_angle_d0.5847410
X-RAY DIFFRACTIONf_chiral_restr0.041811
X-RAY DIFFRACTIONf_plane_restr0.004944
X-RAY DIFFRACTIONf_dihedral_angle_d9.7523302
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3128X-RAY DIFFRACTION9.164TORSIONAL
12B3128X-RAY DIFFRACTION9.164TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.554-2.67020.34221230.2743241388
2.6702-2.8110.30951490.2456266898
2.811-2.98710.27361350.2464269998
2.9871-3.21770.31481370.2395266698
3.2177-3.54140.2751470.2026270498
3.5414-4.05350.22191400.1718269998
4.0535-5.10580.19131390.1553271099
5.1058-44.5850.22561420.1827271599
Refinement TLS params.Method: refined / Origin x: 16.2644 Å / Origin y: 7.1797 Å / Origin z: -38.1372 Å
111213212223313233
T0.1935 Å2-0.0011 Å2-0.0017 Å2-0.2159 Å20.0293 Å2--0.2815 Å2
L0.4255 °20.0114 °20.0494 °2-0.549 °20.498 °2--1.3625 °2
S0.0763 Å °0.03 Å °-0.0448 Å °0.0466 Å °-0.0054 Å °-0.0016 Å °0.0739 Å °-0.0287 Å °-0.0699 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 351
2X-RAY DIFFRACTION1allB9 - 351
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD2 - 4
5X-RAY DIFFRACTION1allS1 - 79

+
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