[English] 日本語
Yorodumi
- PDB-6nn4: The structure of human liver pyruvate kinase, hLPYK-D499N, in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nn4
TitleThe structure of human liver pyruvate kinase, hLPYK-D499N, in complex with Fru-1,6-BP
ComponentsPyruvate kinase PKLR
KeywordsTRANSFERASE / pyruvate kinase / allosteric / glycolysis
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to cAMP / response to glucose / response to nutrient / cellular response to epinephrine stimulus / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / PHOSPHOENOLPYRUVATE / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMcFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Fenton, A.W. / Lamb, A.L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM115340 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM127655 United States
National Science Foundation (NSF, United States)CHE1403293 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)T32GM08545 United States
American Heart AssociationPRE33960374 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-pi bond.
Authors: McFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Chilton, A. / Fenton, A.W. / Lamb, A.L.
History
DepositionJan 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 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 PKLR
B: Pyruvate kinase PKLR
C: Pyruvate kinase PKLR
D: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,72019
Polymers234,2534
Non-polymers2,46715
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22210 Å2
ΔGint-90 kcal/mol
Surface area56610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.572, 204.662, 112.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-711-

HOH

21C-740-

HOH

31D-736-

HOH

-
Components

#1: Protein
Pyruvate kinase PKLR / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver pyruvate kinase


Mass: 58563.176 Da / Num. of mol.: 4 / Fragment: UNP residues 34-574 / Mutation: D499N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / References: UniProt: P30613, 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 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Description: Crystals grew as rectangular prisms within two days and reached full size within two weeks.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium citrate dibasic, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→39.44 Å / Num. obs: 149968 / % possible obs: 99 % / Redundancy: 4.2 % / Net I/σ(I): 10.4
Reflection shellResolution: 2.15→2.19 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IP7

4ip7


Resolution: 2.15→39.437 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.78
RfactorNum. reflection% reflection
Rfree0.2534 1982 1.33 %
Rwork0.2303 --
obs0.2307 149233 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→39.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12730 0 148 353 13231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113077
X-RAY DIFFRACTIONf_angle_d1.14217687
X-RAY DIFFRACTIONf_dihedral_angle_d17.3387953
X-RAY DIFFRACTIONf_chiral_restr0.0592035
X-RAY DIFFRACTIONf_plane_restr0.0072297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1485-2.20220.41281340.332910216X-RAY DIFFRACTION96
2.2022-2.26180.37371320.300910439X-RAY DIFFRACTION99
2.2618-2.32830.33181430.281210436X-RAY DIFFRACTION99
2.3283-2.40350.33281480.264610274X-RAY DIFFRACTION97
2.4035-2.48940.30191350.242410537X-RAY DIFFRACTION99
2.4894-2.5890.26031430.232510506X-RAY DIFFRACTION99
2.589-2.70680.29161460.236910554X-RAY DIFFRACTION99
2.7068-2.84950.28161410.227410506X-RAY DIFFRACTION99
2.8495-3.02790.24461340.235810419X-RAY DIFFRACTION98
3.0279-3.26160.26071420.231510589X-RAY DIFFRACTION99
3.2616-3.58970.21491490.221810650X-RAY DIFFRACTION99
3.5897-4.10860.21961400.20410526X-RAY DIFFRACTION98
4.1086-5.17460.20291540.192610730X-RAY DIFFRACTION99
5.1746-39.44410.26581410.24410869X-RAY DIFFRACTION97

+
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