[English] 日本語
Yorodumi
- PDB-3nie: Crystal Structure of PF11_0147 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nie
TitleCrystal Structure of PF11_0147
ComponentsMAP2 kinase
KeywordsTRANSFERASE / malaria / MapK / kinase / SGC / Structural Genomics Consortium / structural genomics
Function / homology
Function and homology information


RAF-independent MAPK1/3 activation / Frs2-mediated activation / Signalling to ERK5 / ERKs are inactivated / RAF/MAP kinase cascade / Negative feedback regulation of MAPK pathway / Estrogen-stimulated signaling through PRKCZ / Ca2+ pathway / Negative regulation of MAPK pathway / MAPK6/MAPK4 signaling ...RAF-independent MAPK1/3 activation / Frs2-mediated activation / Signalling to ERK5 / ERKs are inactivated / RAF/MAP kinase cascade / Negative feedback regulation of MAPK pathway / Estrogen-stimulated signaling through PRKCZ / Ca2+ pathway / Negative regulation of MAPK pathway / MAPK6/MAPK4 signaling / Neutrophil degranulation / MAP kinase activity / mitogen-activated protein kinase / MAPK cascade / intracellular signal transduction / protein phosphorylation / signal transduction / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase / Mitogen-activated protein kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. ...Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. / Artz, J.D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of PF11_0147
Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. / Artz, J.D. / Bochkarev, A. / Arrowsmith, C. ...Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / MacKenzie, F. / Kozieradzki, I. / Chau, I. / Lew, J. / Senisterra, G. / Cossar, D. / Amani, M. / Artz, J.D. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Hills, T.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MAP2 kinase
B: MAP2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3104
Polymers100,2982
Non-polymers1,0122
Water1,54986
1
A: MAP2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6552
Polymers50,1491
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6552
Polymers50,1491
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-23 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.388, 107.355, 70.787
Angle α, β, γ (deg.)90.000, 109.650, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MAP2 kinase


Mass: 50148.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: map2 / Plasmid: PEt15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q9GR08, UniProt: Q7KQK7*PLUS
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 3350, 0.175 M disodium tartrate, 2 mM AMPPNP, 4 mM MgCl2, 2 mM TCEP, 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 39641 / Num. obs: 37818 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.432 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3430.33817190.209185.7
2.34-2.383.20.3117580.221190.3
2.38-2.433.40.32518390.221192.1
2.43-2.483.50.28618350.216194.3
2.48-2.533.60.26218940.237194.3
2.53-2.593.70.24918440.234195.3
2.59-2.663.80.20618860.255194.8
2.66-2.733.80.18519010.28195.9
2.73-2.813.90.15718620.285195.5
2.81-2.93.90.13119030.301195.7
2.9-33.90.11318990.359196.2
3-3.123.90.09619120.399196.6
3.12-3.263.90.07819060.45196.6
3.26-3.443.90.06219060.466197.1
3.44-3.653.90.05219380.587197.1
3.65-3.933.80.04419470.604197.3
3.93-4.333.80.0419200.751198.1
4.33-4.953.80.03519740.753198.2
4.95-6.243.80.03219640.642198.6
6.24-503.60.02820110.919198.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3N9X

3n9x


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2537 / WRfactor Rwork: 0.2141 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.788 / SU B: 9.172 / SU ML: 0.219 / SU R Cruickshank DPI: 0.3744 / SU Rfree: 0.2602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1906 5 %RANDOM
Rwork0.2231 ---
obs0.2254 37792 95.02 %-
all-39772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.05 Å2 / Biso mean: 48.6944 Å2 / Biso min: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.06 Å20 Å2-0.53 Å2
2--3.96 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 62 86 5956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226011
X-RAY DIFFRACTIONr_bond_other_d0.0010.023978
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9828178
X-RAY DIFFRACTIONr_angle_other_deg0.86339740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7624.291261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.197151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3231530
X-RAY DIFFRACTIONr_chiral_restr0.070.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_mcbond_it0.6011.53692
X-RAY DIFFRACTIONr_mcbond_other0.0891.51467
X-RAY DIFFRACTIONr_mcangle_it1.11225974
X-RAY DIFFRACTIONr_scbond_it1.36132319
X-RAY DIFFRACTIONr_scangle_it2.2134.52204
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 110 -
Rwork0.349 2298 -
all-2408 -
obs-1719 81.41 %

+
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