[English] 日本語
Yorodumi
- PDB-6ynd: GAPDH purified from the supernatant of HEK293F cells: crystal for... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ynd
TitleGAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4.
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / HEK293F / kifunensine / Cysteine-S-Sulfonic acid
Function / homology
Function and homology information


peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / GAIT complex / peptidyl-cysteine S-nitrosylase activity / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule cytoskeleton / neuron apoptotic process / nuclear membrane / microtubule binding / vesicle / killing of cells of another organism / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.525 Å
AuthorsRoversi, P. / Lia, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
CitationJournal: Wellcome Open Res / Year: 2020
Title: Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid.
Authors: Lia, A. / Dowle, A. / Taylor, C. / Santino, A. / Roversi, P.
History
DepositionApr 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,39521
Polymers289,4348
Non-polymers5,96113
Water29,5271639
1
A: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
E: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0109
Polymers144,7174
Non-polymers2,2935
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16620 Å2
ΔGint-97 kcal/mol
Surface area46280 Å2
MethodPISA
2
B: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,38512
Polymers144,7174
Non-polymers3,6688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-95 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.885, 124.455, 141.986
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / Peptidyl-cysteine S-nitrosylase GAPDH


Mass: 36179.230 Da / Num. of mol.: 8 / Mutation: C152X / Source method: isolated from a natural source
Details: GAPDH with catalytic Cys partially oxidised to Cys-S-Sulfonic Acid
Source: (natural) Homo sapiens (human) / Cell line: HEK293F / Organ: Kidney / Tissue: Epithelium
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical
ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1639 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.34 % / Description: Prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% ...Details: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2019
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.52→140.09 Å / Num. obs: 295271 / % possible obs: 69.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 11.7
Reflection shellResolution: 1.52→1.71 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14763 / CC1/2: 0.608 / Rpim(I) all: 0.444 / Rrim(I) all: 1.161 / % possible all: 12.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PROCORdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8F

1u8f


Resolution: 1.525→140.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.095
Details: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including ...Details: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ratio mixture of Cys and Cys S-Sulfonic acid was initially modelled in Fo-Fc residual density. At each Cys152 site, occupancies for Cys and Cys S-Sulfonic acid were refined and constrained so that they sum up to 1.000 plus or minus 0.005.
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 14686 4.97 %RANDOM
Rwork0.182 ---
obs0.1829 295271 69.4 %-
Displacement parametersBiso mean: 27.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.1084 Å20 Å2-0.0028 Å2
2--0.1391 Å20 Å2
3----0.0306 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.525→140.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20156 0 272 1639 22067
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00842354HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0276777HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12877SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes6906HARMONIC5
X-RAY DIFFRACTIONt_it21324HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2827SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact33311SEMIHARMONIC4
LS refinement shellResolution: 1.525→1.63 Å
RfactorNum. reflection% reflection
Rfree0.2256 332 5.62 %
Rwork0.2091 5574 -
obs--7.56 %

+
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