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

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Basic information

Entry
Database: PDB / ID: 6hxk
TitleStructure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate
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 activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase activity / ATP citrate synthase / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol
Similarity search - Function
ATP-citrate synthase / 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 ...ATP-citrate synthase / 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
CITRATE ANION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,61915
Polymers120,0324
Non-polymers1,58711
Water10,683593
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27820 Å2
ΔGint-153 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.341, 123.890, 139.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 30008.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Before crystallization, the the N-terminal sequence MGSSHHHHHHSSGLVPR was removed by thrombin digestion.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET15b / Details (production host): N-terminal cleavable His-tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P53396, ATP citrate synthase

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Non-polymers , 6 types, 604 molecules

#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na2SO4 pH 6.7 20% PEG3350 Protein sample buffer: 20 mM HEPES pH 7.4 150 mM NaCl supplemented with 50 mM Citrate pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.85→67.34 Å / Num. obs: 100132 / % possible obs: 99.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.12 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.205 / Net I/σ(I): 8.69
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 8.7 / Num. unique obs: 15942 / CC1/2: 0.499 / Rrim(I) all: 1.606 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CCL core module from C. limicola

Resolution: 1.85→61.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4982 4.98 %RANDOM
Rwork0.165 ---
obs0.166 100130 99.7 %-
Displacement parametersBiso mean: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.9164 Å20 Å20 Å2
2---0.1965 Å20 Å2
3----2.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.85→61.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8104 0 107 593 8804
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0131279HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3872SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2537HARMONIC5
X-RAY DIFFRACTIONt_it17236HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion14.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1108SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies33HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19975SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 332 4.62 %
Rwork0.213 6859 -
all0.215 7191 -
obs--98.39 %
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)
10.74520.06720.50063.0523-0.85311.62030.00020.2263-0.119-0.34120.0093-0.0340.062-0.0212-0.00950.00320.01290.0140.009-0.0437-0.0351-37.7994-6.8904-10.7293
20.2338-0.0285-0.06710.71250.10291.2877-0.00040.0502-0.1489-0.0197-0.039-0.00720.09010.04440.0395-0.05250.007-0.006-0.0499-0.01420.0096-34.5479-15.18827.7597
33.3039-1.677-0.66490.96660.26270.2210.073-0.18180.1238-0.07890.0262-0.1326-0.08940.0917-0.0991-0.0335-0.01880.0005-0.0145-0.0030.0279-21.2118-11.841715.9245
43.70440.9666-1.82723.4651-0.04931.5317-0.0715-0.130.07340.08450.11370.238-0.09390.188-0.0422-0.0429-0.0175-0.04630.00240.0073-0.0591-19.5274-23.591822.507
52.53961.96160.01361.1702-0.92571.85680.1132-0.1344-0.21780.0053-0.0091-0.03390.1063-0.011-0.1041-0.07590.02210.0039-0.1153-0.0268-0.0265-25.3748-28.97157.3799
61.0122-0.1226-0.62631.3193-1.38982.77010.0611-0.096-0.13810.0629-0.0959-0.0853-0.00720.12430.0348-0.039-0.0147-0.0051-0.02210.00790.0442-17.2872-23.932513.1209
70.4866-0.2232-0.30550.49050.26020.846-0.02010.045-0.05640.054-0.01510.00970.0264-0.0160.0351-0.01450.0043-0.0023-0.04990.01780.0085-34.4706-8.022618.6649
80.72660.13690.62341.456-0.61381.27440.00390.0379-0.21790.0879-0.02880.09750.12830.0250.0249-0.0275-0.0136-0.0025-0.06820.01670.0225-40.6058-24.586620.6192
90.35550.15750.05030.8952-0.25991.3343-0.0335-0.0134-0.2120.05-0.03050.02470.0883-0.02750.064-0.0249-0.009-0.0036-0.0286-0.03010.0613-47.4634-20.77996.3952
100.3660.31430.63350.90330.28971.4363-0.00420.07-0.0946-0.0393-0.017-0.0469-0.01650.04350.0212-0.02330.01010.0076-0.05040.004-0.0336-35.44492.01554.3868
115.75352.5763-0.6241.3718-0.57390.5592-0.02090.24760.0780.03320.08290.1277-0.0821-0.0539-0.0621-0.07790.00430.0042-0.0547-0.0103-0.0285-58.6856-3.65715.3375
121.3822-0.43080.5062.41860.42390.14310.08520.59580.31330.1242-0.1150.2919-0.378-0.88140.0298-0.00480.2360.01950.34670.05310.1066-73.7199-2.0776-1.5329
136.5033-0.071-3.93243.5447-1.04634.72660.0260.50050.4185-0.1140.23920.4265-0.2894-0.2419-0.2652-0.05610.0614-0.0348-0.05960.0456-0.0422-58.9729-0.7155-8.3698
142.431.1048-2.49633.1118-0.45222.7980.00640.4969-0.091-0.20130.07080.1522-0.0357-0.2599-0.0771-0.0963-0.0239-0.0325-0.004-0.065-0.0093-54.9199-17.8861-6.2744
152.18721.4601-4.07350-0.18345.82780.03771.0470.1098-0.3034-0.01930.122-0.1347-0.555-0.0184-0.08240.0443-0.04850.19470.0041-0.0388-66.7369-8.7945-6.9654
162.117-0.0683-0.43270.17180.24731.71020.04440.1674-0.0478-0.03540.02220.068-0.1696-0.2219-0.0667-0.0870.0135-0.0085-0.0548-0.0315-0.0061-58.6725-12.32924.4766
171.55290.6787-1.22750.8398-0.29971.3937-0.04940.0103-0.1536-0.1024-0.0131-0.0642-0.00720.03260.0625-0.0165-0.00230.0011-0.02550.0023-0.0026-36.8493-5.19182.7361
182.4475-1.12070.55562.0633-0.56200.01380.04910.1359-0.15270.042-0.105-0.01030.0676-0.0558-0.00430.0033-0.0044-0.02530.0299-0.0544-34.578819.61450.222
190.56-0.0539-0.11921.7830.66774.107-0.03050.01690.2443-0.05380.0273-0.0225-0.24060.14160.0032-0.01460.00850.0097-0.05390.04390.0191-36.742430.432410.562
201.04570.05140.38440.6756-0.29531.6261-0.01040.05230.1492-0.0151-0.00540.0428-0.16690.02850.0158-0.0120.0161-0.0023-0.04180.00510.0162-42.863127.383124.8065
210.6116-0.1351-0.06211.12360.23830.7923-0.00070.0103-0.00680.0038-0.0063-0.01740.04950.01060.007-0.034-0.0074-0.0022-0.05660.0137-0.026-34.40533.046526.1688
222.002-1.9902-0.87471.19170.28830.0777-0.020.0638-0.3691-0.1-0.02220.30420.0858-0.08330.0422-0.04120.0106-0.0140.01720.00060.0474-56.469812.282227.5723
234.6934-2.0868-2.909200.80381.14450.055-0.6249-0.8903-0.0712-0.14290.19320.158-0.16890.0879-0.1173-0.0616-0.05510.07150.1410.179-70.416112.711536.4528
243.7996-0.1552.18935.98491.21532.8938-0.086-0.2251-0.45580.38860.20560.49880.1603-0.0003-0.1196-0.1195-0.02480.0188-0.06420.1266-0.0003-55.56789.734541.2409
252.2883-0.78911.69073.2997-2.17773.74560.0701-0.20120.0671-0.0131-0.1051-0.0869-0.0774-0.02950.035-0.0932-0.00050.0093-0.0315-0.0246-0.0486-49.539226.034338.1363
265.0964-1.78370.21771.6374-0.85232.3443-0.0504-0.7353-0.48970.17850.12920.21350.075-0.2369-0.0787-0.0609-0.0258-0.00720.05430.0332-0.0167-57.56918.70736.7181
271.6797-0.77870.31861.1156-0.33560.5171-0.02690.075-0.01520.0606-0.00080.0276-0.0278-0.0380.0277-0.04070.0036-0.0073-0.03830.0082-0.0481-42.484815.581524.3476
280.0050.6527-1.32322.9779-0.05690.01350.1038-0.1296-0.030.2933-0.04040.01960.09090.1344-0.06340.05980.0077-0.0119-0.02550.0315-0.0198-35.4858-14.082430.5129
290.2533-0.1242-0.3494.90160.52081.4679-0.0394-0.18570.06880.27250.02790.07770.0915-0.01440.0115-0.0205-0.0002-0.01130.0031-0.0058-0.0336-34.216812.522541.4226
300.48620.09040.31460.47760.22251.0332-0.0038-0.02390.074-0.011-0.0158-0.019-0.00760.0260.0196-0.04590.00170.0009-0.0480.0087-0.0237-33.229917.567420.7136
313.7214-0.70610.75381.3232-0.31280.30960.13520.40320.1287-0.1107-0.1728-0.29820.210.21950.0376-0.0590.02480.0380.04970.07730.0138-9.866416.856713.9029
327.0946-3.07491.01425.7593-2.9544.6711-0.01520.6119-0.0912-0.25660.15010.10690.3063-0.0386-0.1349-0.1013-0.00940.05010.04350.0584-0.0906-15.79324.76346.205
338.3265-1.93492.31711.23-1.20196.81020.23860.39640.61-0.0218-0.0793-0.2195-0.11720.1868-0.1593-0.104-0.03830.0116-0.15010.05560.0466-19.954232.146821.8847
340.5790.1792-0.01620.8949-0.59480.83780.08620.120.2588-0.13-0.1228-0.1701-0.01310.04670.0365-0.01460.01410.02420.06670.08560.0683-13.004825.483616.2404
350.48390.16120.240.29960.08380.64060.00410.0306-0.0357-0.06710.0138-0.0356-0.00150.0379-0.018-0.0403-0.00070.0026-0.04810.0211-0.0308-33.172713.426212.4983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|837 - A|867 }
2X-RAY DIFFRACTION2{ A|868 - A|915 }
3X-RAY DIFFRACTION3{ A|916 - A|965 }
4X-RAY DIFFRACTION4{ A|966 - A|984 }
5X-RAY DIFFRACTION5{ A|985 - A|1001 }
6X-RAY DIFFRACTION6{ A|1002 - A|1039 }
7X-RAY DIFFRACTION7{ A|1040 - A|1098 }
8X-RAY DIFFRACTION8{ B|837 - B|867 }
9X-RAY DIFFRACTION9{ B|868 - B|896 }
10X-RAY DIFFRACTION10{ B|897 - B|930 }
11X-RAY DIFFRACTION11{ B|931 - B|952 }
12X-RAY DIFFRACTION12{ B|953 - B|965 }
13X-RAY DIFFRACTION13{ B|966 - B|984 }
14X-RAY DIFFRACTION14{ B|985 - B|1001 }
15X-RAY DIFFRACTION15{ B|1002 - B|1017 }
16X-RAY DIFFRACTION16{ B|1018 - B|1055 }
17X-RAY DIFFRACTION17{ B|1056 - B|1079 }
18X-RAY DIFFRACTION18{ B|1080 - B|1097 }
19X-RAY DIFFRACTION19{ C|837 - C|867 }
20X-RAY DIFFRACTION20{ C|868 - C|896 }
21X-RAY DIFFRACTION21{ C|897 - C|930 }
22X-RAY DIFFRACTION22{ C|931 - C|952 }
23X-RAY DIFFRACTION23{ C|953 - C|965 }
24X-RAY DIFFRACTION24{ C|966 - C|984 }
25X-RAY DIFFRACTION25{ C|985 - C|1001 }
26X-RAY DIFFRACTION26{ C|1002 - C|1039 }
27X-RAY DIFFRACTION27{ C|1040 - C|1079 }
28X-RAY DIFFRACTION28{ C|1080 - C|1096 }
29X-RAY DIFFRACTION29{ D|837 - D|867 }
30X-RAY DIFFRACTION30{ D|868 - D|930 }
31X-RAY DIFFRACTION31{ D|931 - D|965 }
32X-RAY DIFFRACTION32{ D|966 - D|984 }
33X-RAY DIFFRACTION33{ D|985 - D|1001 }
34X-RAY DIFFRACTION34{ D|1002 - D|1039 }
35X-RAY DIFFRACTION35{ D|1040 - D|1096 }

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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

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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

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