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- PDB-6hxm: Structure of the citryl-CoA lyase core module of human ATP citrat... -

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Basic information

Entry
Database: PDB / ID: 6hxm
TitleStructure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and CoASH in space group C2221
ComponentsATP-citrate synthase
KeywordsLYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / acetyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / coenzyme A metabolic process / oxaloacetate metabolic process / negative regulation of ferroptosis / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / acetyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / coenzyme A metabolic process / oxaloacetate metabolic process / negative regulation of ferroptosis / cholesterol biosynthetic process / lipid biosynthetic process / azurophil granule lumen / fatty acid biosynthetic process / ficolin-1-rich granule lumen / ciliary basal body / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
ATP-citrate synthase / : / ATP-citrate synthase ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site ...ATP-citrate synthase / : / ATP-citrate synthase ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
COENZYME A / CITRATE ANION / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVerstraete, K. / Verschueren, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders1524918N Belgium
CitationJournal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9296
Polymers60,0162
Non-polymers1,9134
Water7,891438
1
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules

A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,85912
Polymers120,0324
Non-polymers3,8278
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area30770 Å2
ΔGint-160 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.829, 111.192, 143.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / ACL / Citrate cleavage enzyme


Mass: 30008.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Prior the crystallization experiments, the N-terminal sequence MGSSHHHHHHSSGLVPR was removed by thrombin digestion.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53396, ATP citrate synthase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Na/K phosphate pH 5.5 0.1 M RbCl 0.1 M Na-citrate pH 5.5 25% PEG Smear Medium 25% PEG400 Citrate, CoAS Protein sample buffer 20 mM HEPES pH 7.4, 150 mM NaCL supplemented with 50 mM ...Details: 0.1 M Na/K phosphate pH 5.5 0.1 M RbCl 0.1 M Na-citrate pH 5.5 25% PEG Smear Medium 25% PEG400 Citrate, CoAS Protein sample buffer 20 mM HEPES pH 7.4, 150 mM NaCL supplemented with 50 mM citrate pH 7.4 and 10 mM CoASH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 160720 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.3 % / Biso Wilson estimate: 11.56 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.061 / Rrim(I) all: 0.135 / Net I/σ(I): 12.1
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 25336 / CC1/2: 0.508 / Rpim(I) all: 1.148 / Rrim(I) all: 2.032 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M. soehngenii ACL

Resolution: 1.3→48.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.042 / SU Rfree Blow DPI: 0.042 / SU Rfree Cruickshank DPI: 0.041
RfactorNum. reflection% reflectionSelection details
Rfree0.178 8113 5.05 %RANDOM
Rwork0.167 ---
obs0.167 160728 99.4 %-
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.6676 Å20 Å20 Å2
2--3.6853 Å20 Å2
3---0.9823 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.3→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 122 438 4666
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019189HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0516712HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2115SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1408HARMONIC5
X-RAY DIFFRACTIONt_it9189HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion13.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion593SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies36HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10921SEMIHARMONIC4
LS refinement shellResolution: 1.3→1.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 542 4.81 %
Rwork0.229 10733 -
all0.228 11275 -
obs--94.7 %
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)
10.91590.258-0.25041.96030.00010.18920.02460.01790.11110.04630.01110.0833-0.047-0.0778-0.0357-0.03670.0173-0.0166-0.0219-0.00010.00961.012351.728238.4743
20.26950.2544-0.31932.48940.15090.26830.05520.04480.0304-0.1133-0.04610.2703-0.0633-0.0291-0.009-0.02870.0131-0.0278-0.0067-0.00230.013156.227338.179932.5002
30.4953-0.05060.29740.59340.04630.2777-0.02950.01990.0351-0.08570.0080.0114-0.02720.01380.0216-0.0174-0.0032-0.0128-0.01020.0015-0.019773.765926.055830.9337
40.0002-0.35551.22110.0246-0.35943.1863-0.01630.10220.0037-0.1794-0.08730.06890.01340.22020.10360.0439-0.0141-0.01920.03620.0343-0.052465.253222.05994.7144
51.10770.3910.19471.4065-0.56331.2678-0.00970.07230.0105-0.0701-0.0078-0.04730.04310.07820.0175-0.002-0.0093-0.0189-0.0153-0.0056-0.025966.979616.598220.6926
61.0906-1.10360.07321.2517-0.15920.47240.01410.00780.0282-0.1317-0.08550.24510.022-0.14650.0714-0.0250.0108-0.0571-0.0091-0.01390.0351.755224.59326.1214
70.6817-0.08380.17821.67370.09641.1365-0.0370.03260.0557-0.1304-0.02130.03690.012-0.07850.0584-0.0068-0.005-0.0303-0.02270.0035-0.028659.653122.632117.9315
81.05320.4360.57321.6560.68660-0.00350.00690.13-0.1493-0.02930.156-0.1371-0.0070.03280.0502-0.0048-0.0638-0.01350.041-0.018660.18342.26319.1789
90.5523-0.16590.48330.9137-0.41411.5105-0.0204-0.06-0.02110.05190.01470.0428-0.0326-0.03320.0057-0.0247-0.003-0.0043-0.0026-0.0018-0.019370.657226.428540.7797
100.5504-0.5683-0.35150.73470.32610.64540.0123-0.0552-0.0947-0.0232-0.0151-0.00110.00730.05240.0028-0.01430.0023-0.00860.0062-0.00750.004490.269712.244737.2266
111.205-0.4341-0.09971.51880.34680.43370.0152-0.0499-0.03980.0219-0.02950.10.0542-0.07620.0143-0.028-0.01780.0043-0.01620.0046-0.016362.246215.149141.143
120.6171-0.6348-0.00112.91160.0150.25770.023-0.0141-0.06790.0996-0.03290.27490.0055-0.01610.01-0.0203-0.00880.01970.0047-0.00330.010259.140329.624948.2835
130.5623-0.1983-0.11970.78960.37580.18190.00330.00510.0427-0.00140.0292-0.0296-0.0164-0.0124-0.0325-0.01720.0005-0.008-0.00860.0039-0.010376.865743.151334.4928
140.14080.1958-0.51690.0009-0.10672.3941-0.0273-0.0935-0.00110.0659-0.02410.00170.04380.10230.05140.01910.01480.02070.01960.0002-0.037874.91641.852364.296
151.0749-1.0489-0.39650.9589-0.4681.5248-0.01920.04160.0202-0.13240.0114-0.0356-0.22640.19420.00780.0303-0.0244-0.0102-0.026-0.0158-0.029470.158452.377657.7191
160.54870.452-0.16531.2892-0.29730.879-0.0193-0.10710.10360.0468-0.02820.1868-0.1157-0.14670.0475-0.0080.00090.0258-0.0107-0.01120.00156.260541.947656.2085
170.57460.55610.00891.8849-0.0011.9354-0.0658-0.05010.06340.0520.01620.1169-0.1057-0.01440.0496-0.00650.00440.0099-0.0033-0.0093-0.033365.765744.228761.612
180.4560.0671-0.10770.8758-0.10890.5571-0.0043-0.03980.02930.0850.01230.04610.04510.0121-0.0079-0.01790.00750.0006-0.0172-0.0089-0.033369.212434.361145.7969
192.70851.6011.11240.52630.33670.4488-0.01160.09120.2336-0.0214-0.02730.022-0.06980.00790.0389-0.01720.0001-0.008-0.0311-0.01380.043492.137655.151932.9703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|835 - A|867 }
2X-RAY DIFFRACTION2{ A|868 - A|896 }
3X-RAY DIFFRACTION3{ A|897 - A|952 }
4X-RAY DIFFRACTION4{ A|953 - A|966 }
5X-RAY DIFFRACTION5{ A|967 - A|984 }
6X-RAY DIFFRACTION6{ A|985 - A|1001 }
7X-RAY DIFFRACTION7{ A|1002 - A|1039 }
8X-RAY DIFFRACTION8{ A|1040 - A|1055 }
9X-RAY DIFFRACTION9{ A|1056 - A|1078 }
10X-RAY DIFFRACTION10{ A|1079 - A|1097 }
11X-RAY DIFFRACTION11{ B|836 - B|867 }
12X-RAY DIFFRACTION12{ B|868 - B|896 }
13X-RAY DIFFRACTION13{ B|897 - B|930 }
14X-RAY DIFFRACTION14{ B|931 - B|966 }
15X-RAY DIFFRACTION15{ B|967 - B|984 }
16X-RAY DIFFRACTION16{ B|985 - B|1001 }
17X-RAY DIFFRACTION17{ B|1002 - B|1039 }
18X-RAY DIFFRACTION18{ B|1040 - B|1078 }
19X-RAY DIFFRACTION19{ B|1079 - B|1100 }

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