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- PDB-1w88: The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) b... -

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Basic information

Entry
Database: PDB / ID: 1w88
TitleThe crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2
Components
  • (PYRUVATE DEHYDROGENASE E1 COMPONENT, ...) x 2
  • DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
KeywordsOXIDOREDUCTASE / PYRUVATE DEHYDROGENASE / DIHYDROLIPOYL / ACETYL TRANSFERASE / MULTIENZYME COMPLEX / TRANSFERASE / CATALYSIS / SLINKY
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
THIAMINE DIPHOSPHATE / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase E1 component subunit alpha / Pyruvate dehydrogenase E1 component subunit beta
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFrank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F.
Citation
Journal: Science / Year: 2004
Title: A Molecular Switch and Proton-Wire Synchronize the Active Sites in Thiamine-Dependent Enzymes
Authors: Frank, R.A.W. / Titman, C.M. / Pratap, J.V. / Luisi, B.F. / Perham, R.N.
#1: Journal: To be Published
Title: Molecular Assembly of a Multi-Enzymes Complex: The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2
Authors: Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F.
History
DepositionSep 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
B: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
C: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
D: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
E: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
F: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
G: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
H: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
I: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
J: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,32018
Polymers317,52210
Non-polymers1,7988
Water21,1321173
1
A: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
B: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
C: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
D: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
I: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,6609
Polymers158,7615
Non-polymers8994
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
F: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
G: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
H: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
J: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,6609
Polymers158,7615
Non-polymers8994
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.180, 133.690, 245.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H
13I
23J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A5 - 367
2112C5 - 367
3112E5 - 367
4112G5 - 367
1121B1 - 324
2121D1 - 324
3121F1 - 324
4121H1 - 324
1131I128 - 168
2131J128 - 168

NCS ensembles :
ID
1
2
3
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

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PYRUVATE DEHYDROGENASE E1 COMPONENT, ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT


Mass: 41385.008 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P21873, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein
PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT


Mass: 35364.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P21874, pyruvate dehydrogenase (acetyl-transferring)

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Protein/peptide , 1 types, 2 molecules IJ

#3: Protein/peptide DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE / E2 / DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX


Mass: 5262.105 Da / Num. of mol.: 2
Fragment: PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 127-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase

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Non-polymers , 3 types, 1181 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1173 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION ASP 180 ASN AND GLU 183 GLN IN CHAINS A, C, E AND G

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49.6 %
Description: MOLECULAR REPLACEMENT WAS CARRIED OUT WITH WILD- TYPE STRUCTURE
Crystal growpH: 5 / Details: 15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 176574 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 32.4
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 7.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W85

1w85


Resolution: 2.3→19.98 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FOLLOWING TERMINAL RESIDUES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY MAP AND ARE NOT MODELLED: A1-A4, A368, C1-C4, E1-E4, G1-G4, I122-I127, I168-I170, J122-J127, J170. IN ...Details: THE FOLLOWING TERMINAL RESIDUES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY MAP AND ARE NOT MODELLED: A1-A4, A368, C1-C4, E1-E4, G1-G4, I122-I127, I168-I170, J122-J127, J170. IN ADDITION, THE FOLLOWING RESIDUES COULD NOT BE MODELLED: A269-A291, C269-C289, E206- E215, E266-E291, F81-F86, F120-F127, G206-G212, G266-G291, H122-H128. FURTHER, THE ELECTRON DENSITY FOR THE SECOND E1-E2 PSBD COMPLEX (CORRESPONDING TO CHAINS E, F, G, H AND J) IN THE ASYMMETRIC UNIT IS NOT AS WELL DEFINED AS THE FIRST (CORRESPONDING TO CHAINS A, B, C, D AND I)
RfactorNum. reflection% reflectionSelection details
Rfree0.262 6705 5 %RANDOM
Rwork0.199 ---
obs0.202 128160 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20626 0 108 1173 21907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02221157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.97128702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07452688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64324.492944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49153476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.73615133
X-RAY DIFFRACTIONr_chiral_restr0.0830.23228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216162
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.210396
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.214621
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.281513421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.332621496
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.92957736
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2467.57204
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
11A1160tight positional0.360.05
12C1160tight positional0.360.05
13E1160tight positional0.40.05
14G1160tight positional0.390.05
21B2207tight positional0.270.05
22D2207tight positional0.290.05
23F2207tight positional0.250.05
24H2207tight positional0.240.05
31I280tight positional0.20.05
11A1084medium positional0.490.5
12C1084medium positional0.490.5
13E1084medium positional0.630.5
14G1084medium positional0.520.5
11A1160tight thermal3.80.5
12C1160tight thermal5.480.5
13E1160tight thermal4.350.5
14G1160tight thermal2.950.5
21B2207tight thermal4.760.5
22D2207tight thermal3.510.5
23F2207tight thermal2.950.5
24H2207tight thermal2.350.5
31I280tight thermal2.220.5
11A1084medium thermal4.972
12C1084medium thermal7.112
13E1084medium thermal6.062
14G1084medium thermal4.322
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 471 -
Rwork0.247 9254 -
obs--99.98 %

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