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- PDB-2onm: Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2... -

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Basic information

Entry
Database: PDB / ID: 2onm
TitleHuman Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with NAD+
ComponentsAldehyde dehydrogenase, mitochondrial precursor
KeywordsOXIDOREDUCTASE / ALDH / NAD / Rossmann Fold
Function / homology
Function and homology information


Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation ...Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANIDINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLarson, H.N. / Hurley, T.D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and functional consequences of coenzyme binding to the inactive asian variant of mitochondrial aldehyde dehydrogenase: roles of residues 475 and 487.
Authors: Larson, H.N. / Zhou, J. / Chen, Z. / Stamler, J.S. / Weiner, H. / Hurley, T.D.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, mitochondrial precursor
B: Aldehyde dehydrogenase, mitochondrial precursor
C: Aldehyde dehydrogenase, mitochondrial precursor
D: Aldehyde dehydrogenase, mitochondrial precursor
E: Aldehyde dehydrogenase, mitochondrial precursor
F: Aldehyde dehydrogenase, mitochondrial precursor
G: Aldehyde dehydrogenase, mitochondrial precursor
H: Aldehyde dehydrogenase, mitochondrial precursor
I: Aldehyde dehydrogenase, mitochondrial precursor
J: Aldehyde dehydrogenase, mitochondrial precursor
K: Aldehyde dehydrogenase, mitochondrial precursor
L: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)662,77875
Polymers653,99612
Non-polymers8,78263
Water34,8051932
1
A: Aldehyde dehydrogenase, mitochondrial precursor
B: Aldehyde dehydrogenase, mitochondrial precursor
C: Aldehyde dehydrogenase, mitochondrial precursor
D: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,93324
Polymers217,9994
Non-polymers2,93420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27470 Å2
ΔGint-137 kcal/mol
Surface area57550 Å2
MethodPISA
2
E: Aldehyde dehydrogenase, mitochondrial precursor
F: Aldehyde dehydrogenase, mitochondrial precursor
G: Aldehyde dehydrogenase, mitochondrial precursor
H: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,59431
Polymers217,9994
Non-polymers3,59627
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28630 Å2
ΔGint-134 kcal/mol
Surface area57280 Å2
MethodPISA
3
I: Aldehyde dehydrogenase, mitochondrial precursor
J: Aldehyde dehydrogenase, mitochondrial precursor
K: Aldehyde dehydrogenase, mitochondrial precursor
L: Aldehyde dehydrogenase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,25120
Polymers217,9994
Non-polymers2,25216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25560 Å2
ΔGint-132 kcal/mol
Surface area57970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.201, 104.854, 162.359
Angle α, β, γ (deg.)78.99, 82.14, 88.55
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a tetramer. There are 3 biological untils in the assymmetric unit. The biological unit 1 consists of chain(s) A, B, C, D. The biological unit 2 consists of chain(s) E, F, G, H. The biological unit 3 consists of chain(s) I, J, K, L.

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Aldehyde dehydrogenase, mitochondrial precursor / ALDH class 2 / ALDHI / ALDH-E2


Mass: 54499.695 Da / Num. of mol.: 12 / Mutation: E487K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)

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Non-polymers , 6 types, 1995 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1932 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 100 mM ACES (N-[2-Acetamido]-2-aminoethane sulfonic acid), 10mM MgCl2, 100 mM Guanidine HCl, 15% w/v PEG 6000, 8mM DTT, pH 6.8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 29, 2005
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→48.95 Å / Num. all: 213379 / Num. obs: 208258 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 50.682 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.01 / Net I/σ(I): 9.1 / Scaling rejects: 3067
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2 / Num. measured all: 40530 / Num. unique all: 20681 / Χ2: 1.08 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O05

1o05


Resolution: 2.5→44.01 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.791 / Data cutoff high absF: 2764167 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 10463 5.1 %RANDOM
Rwork0.23 ---
all0.233 213766 --
obs0.233 206285 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.95 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å20 Å2-2.83 Å2
2---5.48 Å20.78 Å2
3---9.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45576 0 616 1932 48124
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.5-2.520.3931700.34732243394
2.52-2.530.3492350.33538944129
2.53-2.550.3632110.31339264137
2.55-2.570.332090.29439144123
2.57-2.590.3431910.29839444135
2.59-2.610.3282200.29439334153
2.61-2.630.3421980.29739054103
2.63-2.650.3361970.29339554152
2.65-2.670.3482220.339564178
2.67-2.690.3562090.30939204129
2.69-2.720.3332280.29738964124
2.72-2.740.3472040.29539234127
2.74-2.760.3082200.27540024222
2.76-2.790.321940.27238824076
2.79-2.820.3342210.2739584179
2.82-2.840.3252190.26839174136
2.84-2.870.2932020.25539574159
2.87-2.90.3592240.26739414165
2.9-2.930.3062080.24439874195
2.93-2.960.3112100.25338914101
2.96-30.3272060.25140344240
3-3.030.2651780.21639074085
3.03-3.070.31930.24439994192
3.07-3.110.3051970.2439604157
3.11-3.150.3191940.24239184112
3.15-3.190.2872190.23539994218
3.19-3.240.2762250.23838824107
3.24-3.290.2832160.23539804196
3.29-3.340.3052050.24439544159
3.34-3.390.2971910.23539714162
3.39-3.450.252130.21739494162
3.45-3.510.2621960.22340154211
3.51-3.580.3491630.3236983861
3.58-3.650.3832000.33837893989
3.65-3.730.4041990.33438044003
3.73-3.820.2932210.24637553976
3.82-3.920.2672280.21339384166
3.92-4.020.2522370.21538954132
4.02-4.140.2552210.20139314152
4.14-4.270.2262270.18739414168
4.27-4.430.2262400.18739654205
4.43-4.60.222390.18439524191
4.6-4.810.1931840.16440204204
4.81-5.070.1922330.15639234156
5.07-5.380.2272130.18339844197
5.38-5.80.2611840.21140104194
5.8-6.380.2841940.23439834177
6.38-7.30.2212000.20339654165
7.3-9.180.1922470.16539034150
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3parameter.nad
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5cro-gnd-egy.par

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