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- PDB-6qfb: Structure of the human ATP citrate lyase holoenzyme in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6qfb
TitleStructure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A and Mg.ADP
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 / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / coenzyme A metabolic process / oxaloacetate metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / coenzyme A metabolic process / oxaloacetate metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / 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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / ADENOSINE-5'-DIPHOSPHATE / COENZYME A / CITRATE ANION / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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
DepositionJan 9, 2019Deposition 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 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)468,90321
Polymers463,5224
Non-polymers5,38117
Water00
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)469,21324
Polymers463,5224
Non-polymers5,69120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area43640 Å2
ΔGint-284 kcal/mol
Surface area154250 Å2
MethodPISA
2
C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules

C: ATP-citrate synthase
D: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,59218
Polymers463,5224
Non-polymers5,07014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area39800 Å2
ΔGint-263 kcal/mol
Surface area156930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.277, 215.398, 158.421
Angle α, β, γ (deg.)90.00, 117.27, 90.00
Int Tables number5
Space group name H-MC121

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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: 115880.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: pET-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53396, ATP citrate synthase

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Non-polymers , 5 types, 17 molecules

#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION

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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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.15
Details: 17 % PEG 3350 0.2 M Na2HPO4 pH 8.15 Protein sample buffer

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.25→49.03 Å / Num. obs: 99647 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 106.89 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.124 / Net I/σ(I): 11.11
Reflection shellResolution: 3.25→3.45 Å / Redundancy: 4.51 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 15851 / CC1/2: 0.341 / Rrim(I) all: 1.99 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pff, 6hxi

3pff

6hxi


Resolution: 3.25→47.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.193 5084 5.1 %RANDOM
Rwork0.162 ---
obs0.164 99634 99.5 %-
Displacement parametersBiso mean: 137.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.0732 Å20 Å212.2422 Å2
2--0.7271 Å20 Å2
3----2.8003 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 3.25→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31725 0 320 0 32045
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1344348HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11386SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5555HARMONIC5
X-RAY DIFFRACTIONt_it32736HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion19.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance40HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36595SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.27 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2582 117 5.87 %
Rwork0.2386 1876 -
all0.2397 1993 -
obs--94.17 %
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)
15.8727-1.8971-0.93174.43211.6386.3773-0.4346-0.7986-0.11760.39120.3151-0.45380.2890.49580.1196-0.15140.28750.2793-0.0604-0.0307-0.062355.9207-197.182-18.7977
24.8913-2.05940.41955.64760.58712.3445-0.2359-0.3169-1.11670.01180.03310.15910.4153-0.24730.20280.03510.03540.4657-0.1666-0.04470.128934.5309-204.64-23.5625
32.63295.13771.633802.57630.9848-0.1303-0.08840.28280.1671-0.1783-0.29590.0469-0.13880.3086-0.15310.21140.2182-0.0106-0.10270.130347.7587-181.945-28.227
46.3424-1.84294.09064.1341-0.55795.6205-0.1920.39270.8883-0.319-0.1123-1.2435-0.1009-0.19550.3043-0.23940.25120.4712-0.04790.06880.054240.3066-162.724-43.2531
53.1754-1.8769-0.96863.5559-0.12982.19120.15790.8599-0.6042-1.0438-0.40080.10960.1449-0.26720.24290.13660.01520.05260.0865-0.368-0.442114.588-178.819-43.2197
62.4893-3.4055-2.19965.19890.3563-0.25250.23680.338-0.3161-0.50750.1067-0.09820.1835-0.1185-0.34350.13460.15960.13110.16750.2171-0.337811.4318-155.248-45.7025
71.2982-0.05330.31611.87810.21182.13870.0682-0.01080.14740.1132-0.1038-0.1796-0.22520.21030.0356-0.1471-0.0482-0.0794-0.10970.0299-0.107911.6251-143.9055.7783
81.018-0.7102-0.18174.632.65484.9099-0.0534-0.19720.42430.1120.1399-0.0588-0.60870.2032-0.08660.0751-0.1755-0.0468-0.06930.02540.091317.3168-122.87814.1089
94.10490.9693-0.83096.6684-0.33344.7773-0.0424-0.7878-0.09480.0928-0.334-0.8494-0.07370.47170.3764-0.0901-0.19240.1791-0.05460.0921-0.049335.8124-91.542344.3621
104.12721.1521-0.62659.62771.00762.1134-0.31070.07460.352-0.78570.2220.5187-0.22510.07990.08870.2203-0.07560.0755-0.2772-0.0288-0.04714.1774-85.548939.0572
114.3876-1.82991.81520-5.1540.70550.13660.1251-0.35630.0528-0.0141-0.36220.05260.0547-0.12240.0801-0.19430.08340.0075-0.20110.23824.4444-107.20347.3318
123.88360.0222-1.08454.21260.40085.7842-0.1921-0.3979-0.04540.53920.2713-0.33360.72690.9014-0.07920.08110.17190.0048-0.1946-0.1426-0.236312.0608-128.00853.0323
132.09940.98170.18713.37550.91813.2388-0.2763-0.07790.47140.0251-0.03730.7093-0.2433-0.39980.3136-0.14360.08010.0619-0.282-0.16530.0962-10.0631-112.5245.7055
14-1.10320.42232.19036.944.89885.8369-0.14530.07930.47440.40070.43150.44630.14430.2011-0.2862-0.0494-0.27280.31080.1776-0.04740.0275-15.1007-137.29144.9784
152.0145-0.03220.4381.40990.1732.0851-0.05250.11840.2315-0.0215-0.0928-0.2636-0.02480.25920.1453-0.1542-0.02150.0174-0.03950.0239-0.060312.6055-146.6671.2028
161.81420.2424-0.31343.43251.77772.80940.10340.399-0.29-0.28270.0834-0.31530.27290.271-0.1868-0.06910.0769-0.0570.1287-0.001-0.0822.4101-167.578-2.1449
173.4785-2.3077-1.08423.27562.20067.49680.1720.1546-0.98590.9056-0.2716-0.04811.617-0.04440.09960.6520.08070.0238-0.5057-0.2596-0.09092.1214-102.521117.3866
185.6512-1.44411.93836.40091.09635.37850.15520.5497-0.05050.3257-0.1533-0.54981.12190.9586-0.0019-0.05270.211-0.0051-0.0334-0.0659-0.28219.5745-80.9888120.5119
194.93852.303-3.51741.1471-7.1999-4.93850.0301-0.0491-0.23640.13510.09050.28960.1714-0.0453-0.12070.5114-0.12060.042-0.193-0.41-0.1423-12.5657-90.932118.7396
203.9738-1.1751.17428.78812.20131.65330.45120.2508-0.7736-1.0845-0.01851.5440.6487-0.758-0.43270.0668-0.3685-0.52990.1070.22560.4036-36.8035-79.8294124.1169
214.4881-1.06511.65161.9866-0.58113.5792-0.0652-0.39650.03170.3017-0.21560.1325-0.1995-0.45210.2808-0.2524-0.0497-0.041-0.0611-0.166-0.1688-18.3805-55.7976125.0857
224.3026-0.2984.15140.3386-3.06883.13670.2143-0.4858-0.15280.09920.31360.60920.26220.105-0.5279-0.08590.376-0.04990.3424-0.27430.1319-40.9093-50.5227118.7952
232.2569-0.22630.87180.79010.7571.93370.11290.20660.13320.0143-0.0038-0.12730.5944-0.0807-0.1092-0.1634-0.0199-0.2307-0.10730.00310.0877-36.952-64.464368.1856
243.1631-1.08192.69652.01340.1066.58350.33380.08450.0758-0.43050.01310.23610.9-0.6389-0.3469-0.0174-0.2723-0.3275-0.04920.12570.0504-55.2919-72.507955.7547
256.32640.9321.84665.43520.68867.3789-0.27030.04041.056-0.1354-0.00750.1814-1.24610.18050.27770.59960.3246-0.0467-0.5414-0.1662-0.0863-95.6851-3.276890.3718
267.8084-1.42110.95946.0739-0.14823.7058-0.1067-0.1609-0.061-0.4316-0.03690.6385-0.7567-0.59040.14360.10680.30940.0659-0.2263-0.108-0.2378-102.645-25.129687.4546
27-1.50296.35261.043.7161-0.15591.621-0.2142-0.00750.3862-0.12480.2019-0.2517-0.10940.01720.01230.0770.31380.132-0.4687-0.0280.4987-82.8158-14.1046100.6732
285.02890.0589-0.376510.7053-3.45882.5087-0.3535-0.10281.0877-0.0327-0.2272-1.13690.05810.25290.5807-0.03040.3782-0.0688-0.3428-0.26840.0419-66.9622-25.4078117.2528
293.8303-1.1287-0.12051.98650.41412.4282-0.1632-0.756-0.12810.6340.18380.291-0.1503-0.1823-0.0206-0.03780.04080.0667-0.27240.06240.0248-80.6377-49.7288105.8934
305.988-3.9935-1.724902.40094.98140.0587-0.4010.0840.26380.5121-0.11120.27390.1779-0.5708-0.07920.3388-0.2386-0.09510.056-0.0624-57.8593-53.7164113.4184
312.4961-0.1652-0.48921.44520.42163.60470.06610.04670.7126-0.03130.07880.1909-0.55940.1412-0.1448-0.3686-0.0155-0.1481-0.20050.02730.3128-33.9403-39.486168.0918
325.5458-0.1552-1.49661.9371-0.94142.84550.508-0.07741.0956-0.2484-0.1934-0.453-0.50060.4859-0.3146-0.2711-0.2082-0.0196-0.2565-0.08790.5201-12.3028-30.295368.1815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|26 - A|115 }
2X-RAY DIFFRACTION2{ A|2 - A|25 A|116 - A|235 }
3X-RAY DIFFRACTION3{ A|236 - A|248 }
4X-RAY DIFFRACTION4{ A|249 - A|425 }
5X-RAY DIFFRACTION5{ A|488 - A|807 }
6X-RAY DIFFRACTION6{ A|808 - A|837 }
7X-RAY DIFFRACTION7{ A|838 - A|936 A|1055 - A|1097 }
8X-RAY DIFFRACTION8{ A|937 - A|1054 }
9X-RAY DIFFRACTION9{ B|26 - B|115 }
10X-RAY DIFFRACTION10{ B|2 - B|25 B|116 - B|235 }
11X-RAY DIFFRACTION11{ B|236 - B|248 }
12X-RAY DIFFRACTION12{ B|249 - B|425 }
13X-RAY DIFFRACTION13{ B|488 - B|807 }
14X-RAY DIFFRACTION14{ B|808 - B|837 }
15X-RAY DIFFRACTION15{ B|838 - B|936 B|1055 - B|1098 }
16X-RAY DIFFRACTION16{ B|937 - B|1054 }
17X-RAY DIFFRACTION17{ C|26 - C|115 }
18X-RAY DIFFRACTION18{ C|2 - C|25 C|116 - C|235 }
19X-RAY DIFFRACTION19{ C|236 - C|248 }
20X-RAY DIFFRACTION20{ C|249 - C|421 }
21X-RAY DIFFRACTION21{ C|488 - C|807 }
22X-RAY DIFFRACTION22{ C|808 - C|837 }
23X-RAY DIFFRACTION23{ C|838 - C|936 C|1055 - C|1095 }
24X-RAY DIFFRACTION24{ C|937 - C|1054 }
25X-RAY DIFFRACTION25{ D|26 - D|115 }
26X-RAY DIFFRACTION26{ D|2 - D|25 D|116 - D|235 }
27X-RAY DIFFRACTION27{ D|236 - D|248 }
28X-RAY DIFFRACTION28{ D|249 - D|425 }
29X-RAY DIFFRACTION29{ D|488 - D|807 }
30X-RAY DIFFRACTION30{ D|808 - D|837 }
31X-RAY DIFFRACTION31{ D|838 - D|936 D|1055 - D|1101 }
32X-RAY DIFFRACTION32{ D|937 - D|1054 }

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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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