[English] 日本語
Yorodumi
- PDB-7qk7: Crystal structure of the APO form of ALDH1A3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qk7
TitleCrystal structure of the APO form of ALDH1A3
ComponentsAldehyde dehydrogenase family 1 member A3
KeywordsOXIDOREDUCTASE / ALDH1A3 / Aldehyde dehydrogenase family 1 member A3 / APO
Function / homology
Function and homology information


nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway ...nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway / righting reflex / retinal metabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / retinol metabolic process / inner ear morphogenesis / thyroid hormone binding / face development / neuromuscular process controlling balance / NAD+ binding / locomotory behavior / protein homotetramerization / positive regulation of apoptotic process / apoptotic process / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Retinaldehyde dehydrogenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.289 Å
AuthorsCastellvi, A. / Farres, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Commun Biol / Year: 2022
Title: Structural and biochemical evidence that ATP inhibits the cancer biomarker human aldehyde dehydrogenase 1A3.
Authors: Castellvi, A. / Pequerul, R. / Barracco, V. / Juanhuix, J. / Pares, X. / Farres, J.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,19410
Polymers116,3732
Non-polymers8218
Water6,431357
1
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules

A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,38820
Polymers232,7464
Non-polymers1,64216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area22900 Å2
ΔGint-38 kcal/mol
Surface area60050 Å2
Unit cell
Length a, b, c (Å)82.960, 90.133, 159.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Aldehyde dehydrogenase family 1 member A3 / Aldehyde dehydrogenase 6 / Retinaldehyde dehydrogenase 3 / RalDH3


Mass: 58186.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A3, ALDH6 / Production host: Escherichia coli (E. coli)
References: UniProt: P47895, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystallization solution consisted of 100 mM BIS-Tris, pH 5.5, 2-2.2 M ammonium sulfate and 5% PEG 400.

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.289→48.44 Å / Num. obs: 53899 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 50.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Net I/σ(I): 11
Reflection shellResolution: 2.29→2.35 Å / Rmerge(I) obs: 1.391 / Num. unique obs: 4253 / CC1/2: 0.734

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fhz

5fhz


Resolution: 2.289→48.44 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2559 4.75 %RANDOM
Rwork0.1903 ---
obs0.1921 53879 98.7 %-
Displacement parametersBiso mean: 56.55 Å2
Baniso -1Baniso -2Baniso -3
1--26.4426 Å20 Å20 Å2
2--7.693 Å20 Å2
3---18.7496 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.289→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 0 54 357 7770
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087605HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9810313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2582SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1286HARMONIC5
X-RAY DIFFRACTIONt_it7605HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion17.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1016SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6129SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.31 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3538 -3.99 %
Rwork0.2403 1035 -
all0.2442 1078 -
obs--90.5 %

+
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