[English] 日本語
Yorodumi
- PDB-6qun: Crystal structure of AtGapC1 with the catalytic Cys149 irreversib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qun
TitleCrystal structure of AtGapC1 with the catalytic Cys149 irreversibly oxidized by H2O2 treatment
ComponentsGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
KeywordsOXIDOREDUCTASE / Rossman fold / NAD binding / Glycolytic process / oxidative stress / Hydrogen peroxide
Function / homology
Function and homology information


fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / seed development / salicylic acid binding / response to sucrose / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / apoplast / plant-type vacuole / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope ...fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / seed development / salicylic acid binding / response to sucrose / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / apoplast / plant-type vacuole / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope / response to redox state / chloroplast / gluconeogenesis / glycolytic process / response to hydrogen peroxide / NAD binding / NADP binding / response to heat / response to oxidative stress / copper ion binding / positive regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFermani, S. / Zaffagnini, M. / Falini, G. / Trost, P.
Funding support Italy, 1items
OrganizationGrant numberCountry
FARB2012-University of Bologna Italy
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.
Authors: Zaffagnini, M. / Marchand, C.H. / Malferrari, M. / Murail, S. / Bonacchi, S. / Genovese, D. / Montalti, M. / Venturoli, G. / Falini, G. / Baaden, M. / Lemaire, S.D. / Fermani, S. / Trost, P.
History
DepositionFeb 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,09911
Polymers73,0992
Non-polymers1,9999
Water59433
1
O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules

O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,19722
Polymers146,1994
Non-polymers3,99918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Buried area22310 Å2
ΔGint-318 kcal/mol
Surface area45810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.677, 77.677, 407.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11O-404-

SO4

-
Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic / NAD-dependent glyceraldehydephosphate dehydrogenase C subunit 1


Mass: 36549.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The catalytic cysteine is oxidated to sulphinic acid
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPC1, GAPC, GAPDH, At3g04120, T6K12.26 / Production host: Escherichia coli (E. coli)
References: UniProt: P25858, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.0 M (NH4)2SO4, 0.1 M Hepes-NaOH (pH 7.5), 0.1 mM H2O2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.26 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2012
Details: Cilindrical Mirror with 50 nm Pt-coating, oridal Mirros with 50 nm Pt-coating
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 3→47.79 Å / Num. obs: 15798 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 62.2 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.043 / Rrim(I) all: 0.12 / Net I/σ(I): 13.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2164 / Rpim(I) all: 0.168 / Rrim(I) all: 0.483 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0H

4z0h


Resolution: 3→47.785 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / Phase error: 29.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2918 1371 4.99 %random selection
Rwork0.2279 ---
obs0.231 15739 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.9 Å2
Refinement stepCycle: LAST / Resolution: 3→47.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 15 33 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045360
X-RAY DIFFRACTIONf_angle_d0.9327276
X-RAY DIFFRACTIONf_dihedral_angle_d6.1923186
X-RAY DIFFRACTIONf_chiral_restr0.057832
X-RAY DIFFRACTIONf_plane_restr0.007906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.10740.44811160.34112661X-RAY DIFFRACTION100
3.1074-3.23180.33771570.29432555X-RAY DIFFRACTION100
3.2318-3.37890.34221330.27292620X-RAY DIFFRACTION100
3.3789-3.55690.34561580.28312573X-RAY DIFFRACTION100
3.5569-3.77970.3151350.26422586X-RAY DIFFRACTION100
3.7797-4.07140.33041580.24372649X-RAY DIFFRACTION100
4.0714-4.48090.28371200.19872587X-RAY DIFFRACTION100
4.4809-5.12860.22331280.18072643X-RAY DIFFRACTION100
5.1286-6.4590.29081220.20352634X-RAY DIFFRACTION100
6.459-47.79120.21741440.18212597X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.4077 Å / Origin y: 37.11 Å / Origin z: 236.3742 Å
111213212223313233
T0.4902 Å2-0.0776 Å2-0.0111 Å2-0.6789 Å20.0345 Å2--0.3243 Å2
L0.768 °2-0.2203 °20.0211 °2-0.8754 °20.3847 °2--3.0027 °2
S0.0272 Å °0.1189 Å °0.176 Å °0.0492 Å °-0.1132 Å °0.1724 Å °-0.5829 Å °-0.5358 Å °0.1271 Å °
Refinement TLS groupSelection details: (chain O and resseq 0:337) or (chain R and resseq 0:337)

+
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