[English] 日本語
Yorodumi
- PDB-3dv0: Snapshots of catalysis in the E1 subunit of the pyruvate dehydrog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dv0
TitleSnapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Components
  • (Pyruvate dehydrogenase E1 component subunit ...) x 2
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
KeywordsOXIDOREDUCTASE/TRANSFERASE / Oxidoreductase / PYRUVATE / DEHYDROGENASE / DIHYDROLIPOYL / ACETYL TRANSFERASE / MULTIENZYME COMPLEX / TRANSFERASE / Glycolysis / Phosphoprotein / Thiamine pyrophosphate / Acyltransferase / OXIDOREDUCTASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / branched-chain amino acid catabolic process / cytoplasm
Similarity search - Function
Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha / E3-binding domain / : / Dihydrolipoamide Transferase / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Peripheral subunit-binding domain / e3 binding domain ...Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha / E3-binding domain / : / Dihydrolipoamide Transferase / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / Transketolase, C-terminal domain / Rossmann fold - #920 / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Biotin-requiring enzyme / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / Thiamin diphosphate-binding fold / Few Secondary Structures / Irregular / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PYRUVIC ACID / Chem-TPW / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase E1 component subunit alpha / Pyruvate dehydrogenase E1 component subunit beta
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPei, X.Y. / Titman, C.M. / Frank, R.A.W. / Leeper, F.J. / Luisi, B.F.
CitationJournal: Structure / Year: 2008
Title: Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex
Authors: Pei, X.Y. / Titman, C.M. / Frank, R.A. / Leeper, F.J. / Luisi, B.F.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component subunit alpha
B: Pyruvate dehydrogenase E1 component subunit beta
C: Pyruvate dehydrogenase E1 component subunit alpha
D: Pyruvate dehydrogenase E1 component subunit beta
E: Pyruvate dehydrogenase E1 component subunit alpha
F: Pyruvate dehydrogenase E1 component subunit beta
G: Pyruvate dehydrogenase E1 component subunit alpha
H: Pyruvate dehydrogenase E1 component subunit beta
I: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
J: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,01126
Polymers400,84010
Non-polymers2,17216
Water17,835990
1
A: Pyruvate dehydrogenase E1 component subunit alpha
B: Pyruvate dehydrogenase E1 component subunit beta
C: Pyruvate dehydrogenase E1 component subunit alpha
D: Pyruvate dehydrogenase E1 component subunit beta
I: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,59414
Polymers200,4205
Non-polymers1,1749
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23630 Å2
ΔGint-144 kcal/mol
Surface area43430 Å2
MethodPISA
2
E: Pyruvate dehydrogenase E1 component subunit alpha
F: Pyruvate dehydrogenase E1 component subunit beta
G: Pyruvate dehydrogenase E1 component subunit alpha
H: Pyruvate dehydrogenase E1 component subunit beta
J: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,41812
Polymers200,4205
Non-polymers9987
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-144 kcal/mol
Surface area43950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.312, 232.820, 92.004
Angle α, β, γ (deg.)90.00, 91.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H
13I
23J

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSERAA4 - 3675 - 368
21THRTHRLYSLYSCC4 - 3685 - 369
31THRTHRSERSEREE4 - 3675 - 368
41THRTHRSERSERGG4 - 3675 - 368
12ALAALAPHEPHEBB1 - 3242 - 325
22ALAALAPHEPHEDD1 - 3242 - 325
32ALAALAPHEPHEFF1 - 3242 - 325
42ALAALAPHEPHEHH1 - 3242 - 325
13VALVALALAALAII129 - 168129 - 168
23VALVALALAALAJJ129 - 168129 - 168

NCS ensembles :
ID
1
2
3

-
Components

-
Pyruvate dehydrogenase E1 component subunit ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Pyruvate dehydrogenase E1 component subunit alpha


Mass: 41518.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pdhA / Plasmid: pKBstE1a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 recO
References: UniProt: P21873, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein
Pyruvate dehydrogenase E1 component subunit beta


Mass: 35495.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pdhB / Plasmid: pKBstE1b / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 recO
References: UniProt: P21874, pyruvate dehydrogenase (acetyl-transferring)

-
Protein , 1 types, 2 molecules IJ

#3: Protein Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / E2 / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex


Mass: 46392.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pdhC / Plasmid: pKBstE1a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 recO
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase

-
Non-polymers , 5 types, 1006 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-TPW / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / 3-DEAZA-THDP


Mass: 423.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H19N3O7P2S
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→85 Å / Num. all: 110903 / Num. obs: 110687 / % possible obs: 87.5 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4.8 % / Rmerge(I) obs: 0.098 / Rsym value: 0.11 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.48 / % possible all: 79.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1w85

1w85


Resolution: 2.5→72.17 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.894 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24052 4664 4.9 %RANDOM
Rwork0.1726 ---
obs0.17594 90417 96.21 %-
all-90276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å2-0.2 Å2
2---0.3 Å20 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.283 Å0.215 Å
Luzzati d res low-2.5 Å
Luzzati sigma a0.281 Å0.267 Å
Refinement stepCycle: LAST / Resolution: 2.5→72.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21519 0 126 990 22635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02222058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.97429864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.13552760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13524.6121019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.371153748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.80915138
X-RAY DIFFRACTIONr_chiral_restr0.0880.23302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.212456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.215561
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.21257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9781.513772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.509222137
X-RAY DIFFRACTIONr_scbond_it9.04338286
X-RAY DIFFRACTIONr_scangle_it11.4494.57727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2672loose positional0.435
12C2672loose positional0.425
13E2672loose positional0.485
14G2672loose positional0.455
21B2488loose positional0.365
22D2488loose positional0.335
23F2488loose positional0.375
24H2488loose positional0.365
31I196loose positional0.575
11A2672loose thermal8.7910
12C2672loose thermal10.5610
13E2672loose thermal14.3910
14G2672loose thermal7.1710
21B2488loose thermal5.1910
22D2488loose thermal8.7510
23F2488loose thermal12.1310
24H2488loose thermal5.8110
31I196loose thermal5.6310
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 258 -
Rwork0.254 5168 -
obs--74.25 %

+
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