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- PDB-12vt: Y318A Human Aconitate Decarboxylase 1 mutant, apo -

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Basic information

Entry
Database: PDB / ID: 12vt
TitleY318A Human Aconitate Decarboxylase 1 mutant, apo
ComponentsCis-aconitate decarboxylase
KeywordsIMMUNE SYSTEM / immune regulatory gene 1 / oncoprotein / metabolism
Function / homology
Function and homology information


cis-aconitate decarboxylase / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / positive regulation of antimicrobial humoral response / negative regulation of toll-like receptor 2 signaling pathway / cellular response to progesterone stimulus / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / cellular response to cocaine / negative regulation of type I interferon production ...cis-aconitate decarboxylase / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / positive regulation of antimicrobial humoral response / negative regulation of toll-like receptor 2 signaling pathway / cellular response to progesterone stimulus / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / cellular response to cocaine / negative regulation of type I interferon production / cellular response to interleukin-1 / cellular response to interferon-beta / embryo implantation / negative regulation of innate immune response / cellular response to tumor necrosis factor / defense response / cellular response to type II interferon / negative regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / defense response to virus / cellular response to lipopolysaccharide / inflammatory response / protein homodimerization activity / mitochondrion
Similarity search - Function
MmgE/PrpD / MmgE/PrpD superfamily / MmgE/PrpD superfamily, domain 1 / MmgE/PrpD superfamily, domain 2 / MmgE/PrpD, N-terminal / MmgE/PrpD, C-terminal / MmgE/PrpD N-terminal domain / MmgE/PrpD C-terminal domain
Similarity search - Domain/homology
ACETATE ION / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsRunge, B. / Monteiro, D.C.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J Struct Biol X / Year: 2026
Title: Robust structural, kinetic and biophysical characterization of wild-type human ACOD1, selected mutants and their interaction with citraconate.
Authors: Runge, B. / Oktay, H. / Fucci, I.J. / Merten, E.M. / Tarasov, S.G. / Fan, L. / Monteiro, D.C.F.
History
DepositionApr 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cis-aconitate decarboxylase
B: Cis-aconitate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3887
Polymers101,1332
Non-polymers2545
Water15,079837
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-51 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.889, 110.165, 76.11
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cis-aconitate decarboxylase / CAD / Aconitate decarboxylase / Aconitate decarboxylase 1 / Cis-aconitic acid decarboxylase / ...CAD / Aconitate decarboxylase / Aconitate decarboxylase 1 / Cis-aconitic acid decarboxylase / Immune-responsive gene 1 protein


Mass: 50566.727 Da / Num. of mol.: 2 / Mutation: Y318A
Source method: isolated from a genetically manipulated source
Details: truncated construct missing disordered regions (1-3 and 462-481)
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOD1, IRG1 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NK06, cis-aconitate decarboxylase

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Non-polymers , 5 types, 842 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 100 mM Tris pH 8.8, 35% PEG 4000, 200 mM CaOAc, 200 nL drops, 2:1 protein:reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92021 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92021 Å / Relative weight: 1
ReflectionResolution: 1.62→34.55 Å / Num. obs: 80794 / % possible obs: 94.4 % / Redundancy: 13.9 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.072 / Rrim(I) all: 0.28 / Net I/σ(I): 8.4
Reflection shellResolution: 1.62→1.82 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.35 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4040 / CC1/2: 0.55 / Rpim(I) all: 0.664 / Rrim(I) all: 2.52 / % possible all: 46.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→34.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.459 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 4198 5.196 %RANDOM
Rwork0.1604 76595 --
all0.163 ---
obs-80793 74.036 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.316 Å2-0 Å20 Å2
2--0.262 Å20 Å2
3---0.054 Å2
Refinement stepCycle: LAST / Resolution: 1.62→34.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7084 0 13 837 7934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127350
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166997
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.80810022
X-RAY DIFFRACTIONr_angle_other_deg0.5381.74116133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.92540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.664101197
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.81710302
X-RAY DIFFRACTIONr_chiral_restr0.0750.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021650
X-RAY DIFFRACTIONr_nbd_refined0.220.21714
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.26699
X-RAY DIFFRACTIONr_nbtor_refined0.180.23620
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2669
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1660.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.232
X-RAY DIFFRACTIONr_nbd_other0.1610.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.264
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2540.22
X-RAY DIFFRACTIONr_mcbond_it0.9741.0283700
X-RAY DIFFRACTIONr_mcbond_other0.9731.0273699
X-RAY DIFFRACTIONr_mcangle_it1.6341.8414631
X-RAY DIFFRACTIONr_mcangle_other1.6341.8424632
X-RAY DIFFRACTIONr_scbond_it1.4361.223650
X-RAY DIFFRACTIONr_scbond_other1.4351.2193649
X-RAY DIFFRACTIONr_scangle_it2.3492.1575380
X-RAY DIFFRACTIONr_scangle_other2.3482.1555378
X-RAY DIFFRACTIONr_lrange_it4.82913.1138761
X-RAY DIFFRACTIONr_lrange_other4.66611.6358475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.6630.41120.26467X-RAY DIFFRACTION0.8683
1.663-1.7080.516120.268325X-RAY DIFFRACTION4.3456
1.708-1.7580.309550.274900X-RAY DIFFRACTION12.644
1.758-1.8110.3121260.2662202X-RAY DIFFRACTION31.4382
1.811-1.8710.283250.2595551X-RAY DIFFRACTION82.889
1.871-1.9360.2573540.2396436X-RAY DIFFRACTION98.363
1.936-2.0090.2573520.216300X-RAY DIFFRACTION99.7002
2.009-2.0910.2373280.1896070X-RAY DIFFRACTION100
2.091-2.1830.2093420.1715855X-RAY DIFFRACTION100
2.183-2.2890.1852560.1545626X-RAY DIFFRACTION100
2.289-2.4130.2142480.1485383X-RAY DIFFRACTION100
2.413-2.5580.1883120.1395047X-RAY DIFFRACTION100
2.558-2.7340.1942540.144771X-RAY DIFFRACTION100
2.734-2.9510.1952260.1484471X-RAY DIFFRACTION100
2.951-3.2310.1882650.1414052X-RAY DIFFRACTION100
3.231-3.6080.1852070.1383744X-RAY DIFFRACTION100
3.608-4.1590.1631770.1373320X-RAY DIFFRACTION100
4.159-5.0750.1751640.1282862X-RAY DIFFRACTION100
5.075-7.1010.2011320.1642234X-RAY DIFFRACTION100
7.101-34.550.169610.1571379X-RAY DIFFRACTION100
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)
11.3435-0.223-0.27950.520.06220.43230.0160.05960.0096-0.0221-0.0082-0.01650.00750.001-0.00790.0471-0.0122-0.00940.0070.0030.002829.5396-7.0175-26.3954
20.5351-0.0091-0.30740.54410.02731.2422-0.0223-0.0239-0.06540.0315-0.01430.03020.0279-0.04970.03650.0487-00.00420.00950.01690.07345.8521-25.8409-3.1472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 503
2X-RAY DIFFRACTION2ALLB4 - 501

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