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- PDB-8g0t: Crystal Structure of Acetyl-CoA synthetase in complex with a cycl... -

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Basic information

Entry
Database: PDB / ID: 8g0t
TitleCrystal Structure of Acetyl-CoA synthetase in complex with a cyclopropyl ester AMP inhibitor from Cryptococcus neoformans H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-YHK / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: Nat Commun / Year: 2025
Title: Discovery and mechanism of a highly selective, antifungal acetyl-CoA synthetase inhibitor.
Authors: Jezewski, A.J. / Alden, K.M. / Propp, J. / Daraji, D.G. / Lail 3rd, C.L. / Heene, M.E. / Fuller, A.J. / Ferreira, J.C. / Liu, L. / Battaile, K.P. / Williams, N.S. / Staker, B.L. / Lovell, S. ...Authors: Jezewski, A.J. / Alden, K.M. / Propp, J. / Daraji, D.G. / Lail 3rd, C.L. / Heene, M.E. / Fuller, A.J. / Ferreira, J.C. / Liu, L. / Battaile, K.P. / Williams, N.S. / Staker, B.L. / Lovell, S. / Hagen, T.J. / Krysan, D.J.
History
DepositionFeb 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Oct 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,7759
Polymers232,4273
Non-polymers1,3486
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.682, 84.785, 105.471
Angle α, β, γ (deg.)113.29, 106.90, 90.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A854QMN0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-YHK / 5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine


Mass: 387.285 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H18N5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 12.5% 8K, 0.2M NaCl, 0.1M K/Na phosphate, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. Plate: Liu-S-058 well A2, HGN1193 cocrystallization (1 mM), Puck: PSL-0704, Cryo: 25% PEG200 + 75% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.45→91.66 Å / Num. obs: 67989 / % possible obs: 98 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.105 / Χ2: 0.97 / Net I/σ(I): 8.1 / Num. measured all: 247316
Reflection shellResolution: 2.45→2.51 Å / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.835 / Num. measured all: 19251 / Num. unique obs: 5045 / CC1/2: 0.789 / Rpim(I) all: 0.495 / Rrim(I) all: 0.972 / Χ2: 1.02 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→25.27 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 35.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 3312 4.88 %
Rwork0.2183 --
obs0.2206 67846 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→25.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15290 0 90 60 15440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215826
X-RAY DIFFRACTIONf_angle_d0.51921558
X-RAY DIFFRACTIONf_dihedral_angle_d11.6025716
X-RAY DIFFRACTIONf_chiral_restr0.0442340
X-RAY DIFFRACTIONf_plane_restr0.0062767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.50561190.36382698X-RAY DIFFRACTION98
2.48-2.520.42731610.34262680X-RAY DIFFRACTION98
2.52-2.560.36221460.33532664X-RAY DIFFRACTION98
2.56-2.60.47081310.33312673X-RAY DIFFRACTION98
2.6-2.650.39991340.32072732X-RAY DIFFRACTION98
2.65-2.70.32271110.3032693X-RAY DIFFRACTION98
2.7-2.750.39331670.32674X-RAY DIFFRACTION98
2.75-2.80.35291430.29542678X-RAY DIFFRACTION98
2.8-2.870.37381320.29172699X-RAY DIFFRACTION98
2.87-2.930.35621830.30142673X-RAY DIFFRACTION98
2.93-30.36241420.28442680X-RAY DIFFRACTION98
3-3.090.36291270.26872685X-RAY DIFFRACTION98
3.09-3.180.27711210.26212719X-RAY DIFFRACTION98
3.18-3.280.27591220.23712725X-RAY DIFFRACTION98
3.28-3.40.29591680.23542690X-RAY DIFFRACTION99
3.4-3.530.29661150.22612735X-RAY DIFFRACTION98
3.53-3.690.24931410.20442634X-RAY DIFFRACTION97
3.69-3.890.21331540.1982659X-RAY DIFFRACTION97
3.89-4.130.22091160.18442627X-RAY DIFFRACTION96
4.13-4.450.22551180.17862694X-RAY DIFFRACTION96
4.45-4.890.20741220.16432641X-RAY DIFFRACTION97
4.89-5.590.23181620.17612739X-RAY DIFFRACTION99
5.59-7.020.23211570.1982714X-RAY DIFFRACTION99
7.02-25.270.18121200.16312728X-RAY DIFFRACTION99
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)
12.7892-2.11790.24233.19090.05444.57980.32910.2006-0.2254-0.604-0.33890.25860.94650.21420.04190.63520.06360.00770.50380.00650.454212.1079-19.2719-15.6904
21.2867-0.1801-1.06021.66890.13231.43810.54440.6607-0.3441-1.3185-0.50670.04471.62720.61440.04761.89270.4993-0.15540.7579-0.2480.636315.2502-28.9511-30.783
31.2703-0.6325-0.82681.83381.26523.81010.69670.8292-0.0653-1.1379-0.59390.18860.6238-0.0841-0.10271.24140.3954-0.14870.8082-0.06880.51477.6866-10.55-35.6882
43.82570.6724-1.12662.87081.85392.06030.59851.2522-0.3455-0.6676-0.4352-0.2870.89450.6934-0.12422.1530.83590.17211.5063-0.02660.818527.2155-20.8514-52.2156
50.1199-0.10880.24543.103-0.19345.66290.24490.49340.209-0.7204-0.4059-0.51010.67890.93960.23581.20020.53460.29041.49820.20390.893331.551-11.4364-38.6019
61.73690.99880.6961.0385-1.05734.74070.0401-0.5204-0.39490.54020.44970.43461.0893-0.2485-0.55891.45490.32090.27271.14720.47611.06132.4022-33.312733.1009
70.6273-0.32650.49341.8907-0.70962.3704-0.2204-0.0945-0.00320.65130.3350.18980.01740.1874-0.10760.63650.23940.13560.7970.10250.537311.623-4.792422.2386
81.2429-0.8011.0942.5443-0.85962.2362-0.2812-0.7085-0.22661.01910.46240.2753-0.1656-0.4298-0.10391.01940.37550.20991.02560.15940.56239.8751-12.374834.43
91.9081-0.6989-0.16161.6104-0.68894.3546-0.1773-0.5484-0.45390.56960.39440.1120.7790.3607-0.2341.21870.39890.08620.88530.12620.630521.1119-32.114829.714
101.91761.53561.81853.9113-0.23614.35370.8144-0.0166-0.14820.1002-0.9009-0.09990.09160.09380.03251.41010.37810.04021.38180.16480.67534.7979-28.411452.7444
112.3141-1.50880.6973.2771-2.45964.22850.1651-0.39990.38760.16470.36520.1939-1.6116-0.7457-0.50451.83620.41980.2351.52290.07930.742835.2555-21.135542.2329
122.1695-1.49070.20212.7391-0.99882.6781-0.2054-0.4749-0.59950.0510.430.7736-0.1297-0.6833-0.03150.2815-0.07010.05580.64870.15280.8095-12.623310.34-2.777
131.4706-0.93792.2914.1214-1.50595.0309-0.2656-0.4029-0.0077-0.10840.3357-0.309-0.0178-0.3497-0.03880.3124-0.1770.05550.62850.05770.69318.350623.1008-8.93
141.377-2.45930.33723.6112-0.34992.1792-0.0232-0.0824-0.3313-0.13470.1980.5414-0.1428-0.1088-0.03330.2161-0.18950.01520.55220.09820.6966-5.814314.3387-7.6133
151.9939-1.8366-0.1623.51520.0091.0282-0.5291-0.6691-0.52360.62340.78281.0113-0.5677-1.0233-0.19480.43350.16250.16980.9870.25240.92-20.809722.11383.172
161.1678-0.1577-1.16514.24880.00492.9306-0.6825-1.1643-0.03750.89251.00660.6283-0.7821-0.9507-0.26941.07640.760.08431.56010.1150.961-23.574734.861911.8008
174.28-1.4307-0.57293.6243-1.9093.9668-0.6786-0.75040.5610.33160.72030.2416-0.6148-0.8922-0.02021.42080.6422-0.14491.1945-0.02040.998-22.982249.48295.2434
182.87761.2531-1.6973.29111.72415.4208-0.5706-0.23050.62060.61970.4388-0.1182-0.75720.17230.12931.03460.3297-0.19240.80440.02670.881-10.801942.57756.0541
191.87690.1977-0.76290.4290.43342.28290.63430.9093-0.9246-1.5654-0.67651.00440.7188-0.2761-0.0621.82770.1322-0.41230.8029-0.11690.96770.1956-31.3498-30.7572
201.8375-1.3440.59163.6026-1.01963.12760.31150.0214-0.3255-0.4626-0.09850.13830.85310.271-0.18560.63810.0899-0.03490.494-0.04770.401813.1658-19.9939-8.4652
212.7738-0.8859-0.13432.1785-0.95032.70.29120.56040.3766-0.3493-0.4376-0.66060.66311.27680.15780.59750.22030.1080.94170.05370.680530.5419-12.4837-10.6524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 269 through 334 )
2X-RAY DIFFRACTION2chain 'B' and (resid 335 through 493 )
3X-RAY DIFFRACTION3chain 'B' and (resid 494 through 555 )
4X-RAY DIFFRACTION4chain 'B' and (resid 556 through 629 )
5X-RAY DIFFRACTION5chain 'B' and (resid 630 through 677 )
6X-RAY DIFFRACTION6chain 'C' and (resid 11 through 74 )
7X-RAY DIFFRACTION7chain 'C' and (resid 75 through 245 )
8X-RAY DIFFRACTION8chain 'C' and (resid 246 through 441 )
9X-RAY DIFFRACTION9chain 'C' and (resid 442 through 579 )
10X-RAY DIFFRACTION10chain 'C' and (resid 580 through 617 )
11X-RAY DIFFRACTION11chain 'C' and (resid 618 through 677 )
12X-RAY DIFFRACTION12chain 'A' and (resid 11 through 205 )
13X-RAY DIFFRACTION13chain 'A' and (resid 206 through 245 )
14X-RAY DIFFRACTION14chain 'A' and (resid 246 through 365 )
15X-RAY DIFFRACTION15chain 'A' and (resid 366 through 526 )
16X-RAY DIFFRACTION16chain 'A' and (resid 527 through 579 )
17X-RAY DIFFRACTION17chain 'A' and (resid 580 through 617 )
18X-RAY DIFFRACTION18chain 'A' and (resid 618 through 677 )
19X-RAY DIFFRACTION19chain 'B' and (resid 11 through 74 )
20X-RAY DIFFRACTION20chain 'B' and (resid 75 through 169 )
21X-RAY DIFFRACTION21chain 'B' and (resid 170 through 268 )

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