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- PDB-12vd: WT Human Aconitate Decarboxylase 1, citraconate-bound -

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Basic information

Entry
Database: PDB / ID: 12vd
TitleWT Human Aconitate Decarboxylase 1, citraconate-bound
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 / cellular response to lipopolysaccharide / defense response to virus / 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
(~{Z})-2-methylbut-2-enedioic acid / DI(HYDROXYETHYL)ETHER / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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.
History
DepositionApr 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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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)101,7477
Polymers101,3182
Non-polymers4295
Water18,4651025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-42 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.189, 110.36, 76.245
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: 50658.820 Da / Num. of mol.: 2
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, 1030 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CIZ / (~{Z})-2-methylbut-2-enedioic acid / CITRACONATE


Mass: 130.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1025 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 42.03 %
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-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.22→33.9 Å / Num. obs: 155814 / % possible obs: 94.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.053 / Rrim(I) all: 0.202 / Net I/σ(I): 10.3
Reflection shellResolution: 1.22→1.45 Å / Redundancy: 12 % / Rmerge(I) obs: 1.98 / Num. unique obs: 7790 / CC1/2: 0.415 / Rpim(I) all: 0.595 / Rrim(I) all: 2.15 / % possible all: 54.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→33.9 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.57 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1793 8014 5.143 %
Rwork0.1506 147799 -
all0.152 --
obs-155813 61.354 %
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: 15.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.199 Å2-0 Å20 Å2
2--0.092 Å20 Å2
3---0.107 Å2
Refinement stepCycle: LAST / Resolution: 1.22→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7098 0 24 1025 8147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167169
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.80910268
X-RAY DIFFRACTIONr_angle_other_deg0.6521.74116530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.334548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.467101234
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.64410311
X-RAY DIFFRACTIONr_chiral_restr0.0950.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021702
X-RAY DIFFRACTIONr_nbd_refined0.2320.21673
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26744
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23711
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2754
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.24
X-RAY DIFFRACTIONr_metal_ion_refined0.2230.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.226
X-RAY DIFFRACTIONr_nbd_other0.190.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.274
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1530.22
X-RAY DIFFRACTIONr_mcbond_it1.0610.6963743
X-RAY DIFFRACTIONr_mcbond_other1.0590.6963743
X-RAY DIFFRACTIONr_mcangle_it1.7311.2494694
X-RAY DIFFRACTIONr_mcangle_other1.731.2494695
X-RAY DIFFRACTIONr_scbond_it2.1130.9453771
X-RAY DIFFRACTIONr_scbond_other2.1130.9453770
X-RAY DIFFRACTIONr_scangle_it3.3561.6175540
X-RAY DIFFRACTIONr_scangle_other3.3561.6175540
X-RAY DIFFRACTIONr_lrange_it5.1210.0919017
X-RAY DIFFRACTIONr_lrange_other5.0239.8648883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.2540.18810.51520X-RAY DIFFRACTION0.1126
1.254-1.2880.94210.44932X-RAY DIFFRACTION0.1823
1.288-1.3250.25340.39655X-RAY DIFFRACTION0.3352
1.325-1.3660.382340.318666X-RAY DIFFRACTION4.0743
1.366-1.4110.3071560.2982873X-RAY DIFFRACTION18.1725
1.411-1.460.2873100.2885508X-RAY DIFFRACTION36.2289
1.46-1.5150.2756370.26711669X-RAY DIFFRACTION79.1637
1.515-1.5770.2597680.23614035X-RAY DIFFRACTION98.6143
1.577-1.6470.2277560.2113573X-RAY DIFFRACTION99.7424
1.647-1.7270.2056810.18413074X-RAY DIFFRACTION99.8258
1.727-1.820.216800.16412384X-RAY DIFFRACTION99.9006
1.82-1.930.1936300.15811817X-RAY DIFFRACTION99.9679
1.93-2.0630.1736030.14211089X-RAY DIFFRACTION100
2.063-2.2280.1535360.13110343X-RAY DIFFRACTION100
2.228-2.4390.1495260.1249550X-RAY DIFFRACTION100
2.439-2.7250.1594410.1218703X-RAY DIFFRACTION100
2.725-3.1440.1583940.1237697X-RAY DIFFRACTION100
3.144-3.8420.1653970.1186526X-RAY DIFFRACTION100
3.842-5.3990.1472940.1165152X-RAY DIFFRACTION100
5.399-33.90.1571650.1513033X-RAY DIFFRACTION99.9687
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)
11.0240.1887-0.21140.4512-0.06020.37190.0091-0.04210.01840.0174-0.00490.0074-0.01-0.0025-0.00410.03640.012-0.00640.0107-0.0040.001821.312-6.9049-11.6826
20.41220.0103-0.22590.4302-0.04950.9402-0.00730.0131-0.0491-0.0217-0.0086-0.02370.02860.04080.01580.04220.0010.00470.0207-0.01170.049445.207-26.0625-35.0502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 1136
2X-RAY DIFFRACTION2ALLB4 - 1091

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