[English] 日本語
Yorodumi
- PDB-4ic8: Crystal structure of the apo ERK5 kinase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ic8
TitleCrystal structure of the apo ERK5 kinase domain
ComponentsMitogen-activated protein kinase 7
KeywordsTRANSFERASE / KINASE / SIGNALING
Function / homology
Function and homology information


Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade / ERK/MAPK targets ...Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade / ERK/MAPK targets / negative regulation of smooth muscle cell apoptotic process / enzyme inhibitor activity / positive regulation of protein metabolic process / RET signaling / MAP kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / JUN kinase activity / mitogen-activated protein kinase / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to transforming growth factor beta stimulus / cellular response to growth factor stimulus / PML body / negative regulation of inflammatory response / cellular response to hydrogen peroxide / adenylate cyclase-activating G protein-coupled receptor signaling pathway / MAPK cascade / Senescence-Associated Secretory Phenotype (SASP) / cell differentiation / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural mechanism for the specific assembly and activation of the extracellular signal regulated kinase 5 (ERK5) module.
Authors: Glatz, G. / Gogl, G. / Alexa, A. / Remenyi, A.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 7
B: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)99,6062
Polymers99,6062
Non-polymers00
Water00
1
A: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)49,8031
Polymers49,8031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)49,8031
Polymers49,8031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 93.220, 69.260
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Mitogen-activated protein kinase 7 / MAP kinase 7 / MAPK 7 / Big MAP kinase 1 / BMK-1 / Extracellular signal-regulated kinase 5 / ERK-5


Mass: 49802.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK7, BMK1, ERK5, PRKM7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13164, mitogen-activated protein kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 200, 100mM MIB, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 31, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.29 Å / Num. all: 18893 / Num. obs: 18522 / % possible obs: 98 % / Observed criterion σ(F): 2.52 / Observed criterion σ(I): 2.52
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.3 % / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.29 Å / σ(F): 1.34 / Phase error: 32.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 953 5.14 %RANDOM
Rwork0.2619 ---
all0.2632 18893 --
obs0.2632 18522 98.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 0 0 4807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064920
X-RAY DIFFRACTIONf_angle_d1.5196731
X-RAY DIFFRACTIONf_dihedral_angle_d18.0411660
X-RAY DIFFRACTIONf_chiral_restr0.098783
X-RAY DIFFRACTIONf_plane_restr0.007881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94850.34611380.32542555X-RAY DIFFRACTION95
2.9485-3.13320.3671320.32522556X-RAY DIFFRACTION95
3.1332-3.3750.34251360.30122542X-RAY DIFFRACTION95
3.375-3.71440.28541310.27382543X-RAY DIFFRACTION95
3.7144-4.25140.29181300.25172197X-RAY DIFFRACTION82
4.2514-5.35440.26421530.23132562X-RAY DIFFRACTION94
5.3544-40.76430.26361280.24112605X-RAY DIFFRACTION95
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)
10.82070.42870.27880.2680.08540.2051-0.31210.6491-0.3715-0.1296-0.0631-0.35870.2049-0.058-0.19970.26380.13140.41170.85060.00581.088833.2808-44.23095.0999
25.14080.0844-0.20371.01011.74763.01690.2104-0.1311-0.27440.1845-0.0967-0.4289-0.0941-0.4285-0.06290.29290.07790.07570.35060.07630.767233.2631-35.54067.9493
31.275-0.519-0.16382.38050.32431.9044-0.3187-0.1459-0.1708-0.22980.2147-0.3851-0.21670.3036-0.00420.61730.0557-0.01540.40920.00920.377331.2668-30.031913.0794
43.741-0.0011.53131.74580.81251.37580.3135-0.1061-0.49360.3571-0.1102-0.6658-0.4253-0.0033-0.01340.5492-0.0383-0.03440.3526-0.03660.367920.7634-22.409318.1961
51.3728-0.1402-0.17780.8881-1.35013.0245-0.1970.1090.2929-0.22330.00760.29390.0923-0.06760.06430.82590.00990.08050.35670.01820.356112.7491-10.815213.1483
63.3508-0.1679-1.27210.4793-0.54053.18340.19280.19070.2488-0.67160.37540.4243-0.1541-0.6310.21040.72560.0291-0.03840.36990.17310.84259.32284.421114.4101
77.09020.82990.99960.76250.70140.7413-0.67840.20350.75130.03420.54870.4632-0.3787-0.32050.04260.5807-0.0750.01110.82530.05940.42664.1369-13.56226.278
83.66750.21580.41731.31731.40681.63860.3423-0.3282-0.18871.32740.5214-0.1501-0.66640.0955-0.07980.70250.0095-0.03360.63390.0220.302516.0317-11.3127.5665
90.3188-0.7172-0.04412.65760.22760.02370.126-0.12770.01130.79650.4143-0.87190.17940.31410.11910.7059-0.0938-0.24511.1428-0.07010.362233.9492-18.555724.2105
102.2255-0.0541-0.01860.8350.51921.4998-0.0913-0.25880.10140.16190.2339-0.51640.08870.61770.29680.14870.1452-0.08080.85370.07150.967546.384-26.12467.7732
112.0581-0.7420.78431.6471-0.35751.0801-0.10550.36890.67630.07770.10490.2471-0.6640.0813-0.13650.5051-0.35120.06820.29040.17270.7548-2.4296-5.4127-30.8904
121.95512.49581.04114.7314-0.01531.7721-0.3016-0.1828-0.0553-0.41650.1960.6818-0.6033-0.34050.06240.37730.1299-0.0250.41210.14230.582-4.5258-16.115-26.4373
132.44991.06030.54573.38780.31122.6663-0.3210.0385-0.2139-0.10650.38160.864-1.03760.13460.03610.64430.24610.17970.33410.09540.5444-7.2385-15.3378-20.1966
144.5782-0.19561.99622.0167-0.19273.36190.0714-0.16520.6589-0.4697-0.00360.131-1.10250.01510.1420.6739-0.11990.08090.20320.05880.39567.7882-14.9124-22.6672
151.960.0163-0.68431.10170.38671.16990.04250.0347-0.1158-0.3782-0.00810.06630.03590.17760.08010.46960.0296-0.03570.50230.06770.338912.7879-30.1453-18.5116
162.4736-2.3133-2.73963.74261.31694.5361-0.09130.1576-0.58820.76180.20930.45750.2960.84710.15710.90.05860.09630.4573-0.09990.803319.541-52.0189-20.0295
172.9053-1.28370.50290.74070.08850.8433-0.4151-0.5969-0.7230.78980.09250.17950.20820.3008-0.15420.68610.2454-0.38410.61150.13530.356713.6493-32.3525-6.72
184.2116-0.74611.09544.7626-2.73051.65840.06170.21560.02330.0173-0.35160.6566-0.1823-0.75440.10420.5632-0.064-0.16310.660.07440.5617-15.9945-24.2976-27.4969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 256 )
6X-RAY DIFFRACTION6chain 'A' and (resid 257 through 286 )
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 305 )
8X-RAY DIFFRACTION8chain 'A' and (resid 306 through 328 )
9X-RAY DIFFRACTION9chain 'A' and (resid 329 through 350 )
10X-RAY DIFFRACTION10chain 'A' and (resid 351 through 368 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 45 )
12X-RAY DIFFRACTION12chain 'B' and (resid 46 through 86 )
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 106 )
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 133 )
15X-RAY DIFFRACTION15chain 'B' and (resid 134 through 256 )
16X-RAY DIFFRACTION16chain 'B' and (resid 257 through 286 )
17X-RAY DIFFRACTION17chain 'B' and (resid 287 through 343 )
18X-RAY DIFFRACTION18chain 'B' and (resid 344 through 368 )

+
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