[English] 日本語
Yorodumi
- PDB-6v0z: Structure of ALDH7A1 mutant R441C complexed with NAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v0z
TitleStructure of ALDH7A1 mutant R441C complexed with NAD
ComponentsAlpha-aminoadipic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / sensory perception of sound / mitochondrial matrix / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsKorasick, D.A. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093123 United States
CitationJournal: Chem.Biol.Interact. / Year: 2024
Title: Biochemical, structural, and computational analyses of two new clinically identified missense mutations of ALDH7A1.
Authors: Korasick, D.A. / Buckley, D.P. / Palpacelli, A. / Cursio, I. / Cesaroni, E. / Cheng, J. / Tanner, J.J.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_ncs_dom_lim
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_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,90017
Polymers444,5308
Non-polymers5,3699
Water29,1841620
1
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,9819
Polymers222,2654
Non-polymers2,7165
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26620 Å2
ΔGint-130 kcal/mol
Surface area59890 Å2
MethodPISA
2
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,9198
Polymers222,2654
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26220 Å2
ΔGint-132 kcal/mol
Surface area60330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.964, 161.647, 158.542
Angle α, β, γ (deg.)90.000, 94.450, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 14 or (resid 15...
21(chain B and (resid 3 through 14 or (resid 15...
31(chain C and (resid 3 through 14 or (resid 15...
41(chain D and (resid 3 through 14 or (resid 15...
51(chain E and (resid 3 through 14 or (resid 15...
61(chain F and (resid 3 through 14 or (resid 15...
71(chain G and (resid 3 through 19 or (resid 20...
81(chain H and (resid 3 through 19 or (resid 20...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resid 3 through 14 or (resid 15...AA3 - 145 - 16
12LYSLYSLYSLYS(chain A and (resid 3 through 14 or (resid 15...AA1517
13THRTHRNADNAD(chain A and (resid 3 through 14 or (resid 15...AA - I3 - 6015
14THRTHRNADNAD(chain A and (resid 3 through 14 or (resid 15...AA - I3 - 6015
15THRTHRNADNAD(chain A and (resid 3 through 14 or (resid 15...AA - I3 - 6015
16THRTHRNADNAD(chain A and (resid 3 through 14 or (resid 15...AA - I3 - 6015
21THRTHRLEULEU(chain B and (resid 3 through 14 or (resid 15...BB3 - 145 - 16
22LYSLYSLYSLYS(chain B and (resid 3 through 14 or (resid 15...BB1517
23THRTHRNADNAD(chain B and (resid 3 through 14 or (resid 15...BB - J3 - 6015
24THRTHRNADNAD(chain B and (resid 3 through 14 or (resid 15...BB - J3 - 6015
25THRTHRNADNAD(chain B and (resid 3 through 14 or (resid 15...BB - J3 - 6015
26THRTHRNADNAD(chain B and (resid 3 through 14 or (resid 15...BB - J3 - 6015
31THRTHRLEULEU(chain C and (resid 3 through 14 or (resid 15...CC3 - 145 - 16
32LYSLYSLYSLYS(chain C and (resid 3 through 14 or (resid 15...CC1517
33THRTHRNADNAD(chain C and (resid 3 through 14 or (resid 15...CC - K3 - 6015
34THRTHRNADNAD(chain C and (resid 3 through 14 or (resid 15...CC - K3 - 6015
35THRTHRNADNAD(chain C and (resid 3 through 14 or (resid 15...CC - K3 - 6015
41THRTHRLEULEU(chain D and (resid 3 through 14 or (resid 15...DD3 - 145 - 16
42LYSLYSLYSLYS(chain D and (resid 3 through 14 or (resid 15...DD1517
43THRTHRNADNAD(chain D and (resid 3 through 14 or (resid 15...DD - M3 - 6015
44THRTHRNADNAD(chain D and (resid 3 through 14 or (resid 15...DD - M3 - 6015
45THRTHRNADNAD(chain D and (resid 3 through 14 or (resid 15...DD - M3 - 6015
46THRTHRNADNAD(chain D and (resid 3 through 14 or (resid 15...DD - M3 - 6015
51THRTHRLEULEU(chain E and (resid 3 through 14 or (resid 15...EE3 - 145 - 16
52LYSLYSLYSLYS(chain E and (resid 3 through 14 or (resid 15...EE1517
53THRTHRNADNAD(chain E and (resid 3 through 14 or (resid 15...EE - N3 - 6015
54THRTHRNADNAD(chain E and (resid 3 through 14 or (resid 15...EE - N3 - 6015
55THRTHRNADNAD(chain E and (resid 3 through 14 or (resid 15...EE - N3 - 6015
61THRTHRLEULEU(chain F and (resid 3 through 14 or (resid 15...FF3 - 145 - 16
62LYSLYSLYSLYS(chain F and (resid 3 through 14 or (resid 15...FF1517
63THRTHRNADNAD(chain F and (resid 3 through 14 or (resid 15...FF - O3 - 6015
71THRTHRLEULEU(chain G and (resid 3 through 19 or (resid 20...GG3 - 195 - 21
72ARGARGGLUGLU(chain G and (resid 3 through 19 or (resid 20...GG20 - 2122 - 23
73THRTHRNADNAD(chain G and (resid 3 through 19 or (resid 20...GG - P3 - 6015
74THRTHRNADNAD(chain G and (resid 3 through 19 or (resid 20...GG - P3 - 6015
75THRTHRNADNAD(chain G and (resid 3 through 19 or (resid 20...GG - P3 - 6015
76THRTHRNADNAD(chain G and (resid 3 through 19 or (resid 20...GG - P3 - 6015
81THRTHRLEULEU(chain H and (resid 3 through 19 or (resid 20...HH3 - 195 - 21
82ARGARGGLUGLU(chain H and (resid 3 through 19 or (resid 20...HH20 - 2122 - 23
83THRTHRNADNAD(chain H and (resid 3 through 19 or (resid 20...HH - Q3 - 6015
84THRTHRNADNAD(chain H and (resid 3 through 19 or (resid 20...HH - Q3 - 6015
85THRTHRNADNAD(chain H and (resid 3 through 19 or (resid 20...HH - Q3 - 6015
86THRTHRNADNAD(chain H and (resid 3 through 19 or (resid 20...HH - Q3 - 6015

-
Components

#1: Protein
Alpha-aminoadipic semialdehyde dehydrogenase / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine ...Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase


Mass: 55566.312 Da / Num. of mol.: 8 / Mutation: R441C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1620 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21% PEG 3350, 0.2 M magnesium chloride, Bis-Tris pH 6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.02→48.073 Å / Num. obs: 252123 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.108 / Rrim(I) all: 0.207 / Net I/σ(I): 6.5
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.646 / Num. measured all: 41141 / Num. unique obs: 12517 / CC1/2: 0.345 / Rpim(I) all: 1.077 / Rrim(I) all: 1.973 / Net I/σ(I) obs: 0.7 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zuk

4zuk


Resolution: 2.02→48.073 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.2488 12316 4.91 %
Rwork0.1937 --
obs0.1964 250997 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.31 Å2 / Biso mean: 29.8094 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 2.02→48.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30792 0 356 1620 32768
Biso mean--31.71 29.81 -
Num. residues----4072
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18753X-RAY DIFFRACTION8.01TORSIONAL
12B18753X-RAY DIFFRACTION8.01TORSIONAL
13C18753X-RAY DIFFRACTION8.01TORSIONAL
14D18753X-RAY DIFFRACTION8.01TORSIONAL
15E18753X-RAY DIFFRACTION8.01TORSIONAL
16F18753X-RAY DIFFRACTION8.01TORSIONAL
17G18753X-RAY DIFFRACTION8.01TORSIONAL
18H18753X-RAY DIFFRACTION8.01TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.0430.37554000.3165769696
2.043-2.0670.3764080.3339767396
2.067-2.09220.34744000.298785898
2.0922-2.11870.34914270.2846803099
2.1187-2.14660.34854330.2771793099
2.1466-2.1760.33594060.26747992100
2.176-2.20710.31844040.25317978100
2.2071-2.240.35734110.2985787298
2.24-2.2750.33224260.2762783298
2.275-2.31230.31854510.2399794799
2.3123-2.35220.30414390.2342790299
2.3522-2.39490.30314330.2278056100
2.3949-2.4410.29234440.22258030100
2.441-2.49080.27224470.21148003100
2.4908-2.5450.28463870.20248056100
2.545-2.60420.25544150.19488030100
2.6042-2.66930.26444290.2048795799
2.6693-2.74150.27314310.20657988100
2.7415-2.82210.25243870.1938057100
2.8221-2.91320.2654100.19588028100
2.9132-3.01730.26064030.19068040100
3.0173-3.13810.25053880.18888048100
3.1381-3.28090.22933780.1735806599
3.2809-3.45380.22923730.1741790698
3.4538-3.67010.21884410.1663784998
3.6701-3.95340.214170.1597781497
3.9534-4.3510.20263110.1489800698
4.351-4.980.1614300.1309790598
4.98-6.27210.19363630.1505809299
6.2721-48.0730.16984240.1579804198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38190.22980.06980.42940.11010.41360.016-0.0093-0.06180.0030.013-0.08930.01670.1001-0.02420.15440.0126-0.00410.1872-0.0460.268756.88358.682533.8721
20.3589-0.10030.03150.6570.12450.43480.0055-0.04820.03910.0506-0.04150.1463-0.0267-0.09780.03430.1521-0.02120.01920.1938-0.04740.247122.464258.286443.2188
30.4351-0.1498-0.08670.37050.05310.3132-0.01360.0938-0.1706-0.0527-0.03170.03450.0316-0.03610.0390.1592-0.00120.00540.1932-0.04230.306345.504418.747123.6224
40.29330.04170.05390.3345-0.12910.58410.0187-0.1115-0.06950.0998-0.0117-0.04690.01820.0336-0.00980.2084-0.0205-0.01890.2210.00410.245136.077320.393357.9193
50.78680.404-0.13930.3767-0.14090.2354-0.02890.0338-0.0082-0.03260.02550.06030.0271-0.0690.0010.1685-0.00010.00250.2012-0.07940.244823.879898.251733.1999
60.3649-0.1226-0.07640.3467-0.02510.35250.0174-0.0304-0.04980.0324-0.017-0.07340.00960.05310.0060.1775-0.0241-0.00960.2318-0.05770.287158.194498.912143.2838
70.407-0.0522-0.03820.4596-0.1140.3580.0011-0.03060.1257-0.0486-0.0140.0856-0.035-0.07270.00490.17980.0108-0.02510.2181-0.06010.327435.4162137.735321.9811
80.5923-0.0038-0.2550.30950.12190.34860.0298-0.19840.10210.11270.0124-0.0028-0.03840.0167-0.04480.2237-0.02170.02240.2627-0.08130.265444.093137.224556.5494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 511)A3 - 511
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 511)B3 - 511
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 511)C3 - 511
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 511)D3 - 511
5X-RAY DIFFRACTION5(chain 'E' and resid 3 through 511)E3 - 511
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 511)F3 - 511
7X-RAY DIFFRACTION7(chain 'G' and resid 3 through 511)G3 - 511
8X-RAY DIFFRACTION8(chain 'H' and resid 3 through 511)H3 - 511

+
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