[English] 日本語
Yorodumi
- PDB-3gr4: Activator-Bound Structure of Human Pyruvate Kinase M2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gr4
TitleActivator-Bound Structure of Human Pyruvate Kinase M2
ComponentsPyruvate kinase isozymes M1/M2
KeywordsTRANSFERASE / activator / Acetylation / Allosteric enzyme / Alternative splicing / Glycolysis / Kinase / Magnesium / Metal-binding / Phosphoprotein / Polymorphism / Pyruvate / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / secretory granule lumen / collagen-containing extracellular matrix / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-DYY / 1,6-di-O-phosphono-beta-D-fructofuranose / L(+)-TARTARIC ACID / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsHong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. ...Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Inglese, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Activator-Bound Structures of Human Pyruvate Kinase M2
Authors: Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Authors: Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Inglese, J. / Park, H.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate kinase isozymes M1/M2
B: Pyruvate kinase isozymes M1/M2
C: Pyruvate kinase isozymes M1/M2
D: Pyruvate kinase isozymes M1/M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,96036
Polymers240,2004
Non-polymers3,75932
Water16,520917
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21360 Å2
ΔGint-109 kcal/mol
Surface area69080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.275, 153.206, 93.138
Angle α, β, γ (deg.)90.000, 102.910, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Pyruvate kinase isozymes M1/M2 / Pyruvate kinase muscle isozyme / Pyruvate kinase 2/3 / Cytosolic thyroid hormone-binding protein / ...Pyruvate kinase muscle isozyme / Pyruvate kinase 2/3 / Cytosolic thyroid hormone-binding protein / CTHBP / THBP1


Mass: 60050.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM2, PK2, PK3, PKM / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P14618, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 945 molecules

#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-DYY / 1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine


Mass: 460.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18F2N2O6S2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 18 / Source method: obtained synthetically
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2M diammonium tartrate, 0.005M activator, 0.005M ADP, vapor diffusion, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 283418 / % possible obs: 96.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Χ2: 1.369 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.662.50.707221121.13775.2
1.66-1.722.90.579263711.06290
1.72-1.83.40.468289901.07798.7
1.8-1.93.80.352294011.158100
1.9-2.023.80.24293391.46299.9
2.02-2.173.80.151293851.58799.9
2.17-2.393.80.093293831.40199.9
2.39-2.743.90.061294371.292100
2.74-3.453.90.05294522.052100
3.45-503.80.026295481.15699.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MolProbitymodel building
prodrgrefinement
RefinementStarting model: isomorphous replacement with pdb entry 3GQY

3gqy


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.2 / SU B: 2.128 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2916 1.04 %thin shells (sftools)
Rwork0.208 ---
obs0.208 280370 96.273 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.294 Å2
Baniso -1Baniso -2Baniso -3
1--0.546 Å20 Å2-0.94 Å2
2---0.011 Å20 Å2
3---0.136 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15294 0 292 917 16503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215834
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210516
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.98521531
X-RAY DIFFRACTIONr_angle_other_deg0.8893.00125640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37552064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87523.725612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.864152590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.46515115
X-RAY DIFFRACTIONr_chiral_restr0.0790.22521
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023025
X-RAY DIFFRACTIONr_mcbond_it1.483210223
X-RAY DIFFRACTIONr_mcbond_other0.43424167
X-RAY DIFFRACTIONr_mcangle_it2.239316389
X-RAY DIFFRACTIONr_scbond_it1.80225611
X-RAY DIFFRACTIONr_scangle_it2.80335132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64100.362158652144173.994
1.641-1.6860.342030.318176742093785.385
1.686-1.7350.3362290.281189672033294.413
1.735-1.7880.2932380.273193161975998.963
1.788-1.8470.2882130.256189111917799.724
1.847-1.9110.2582190.243181251846599.345
1.911-1.9830.2581970.238176201791199.475
1.983-2.0640.2491720.228168961719199.285
2.064-2.1550.2271670.217162731649199.691
2.155-2.260.2311500.218155721581899.393
2.26-2.3810.2281550.203148031504699.415
2.381-2.5240.2372360.201139741423299.845
2.524-2.6970.2361040.2132101333399.857
2.697-2.9120.2251110.208123701251399.744
2.912-3.1860.2091510.212112911146499.808
3.186-3.5580.2231040.198102851041499.76
3.558-4.0980.218600.1729117920299.728
4.098-4.9960.1961150.1447703782399.936
4.996-6.970.215550.1916044610299.951
6.97-300.173370.1863438357297.284

+
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://pdbjlvh1.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