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- EMDB-0567: Cryo-EM structure of human ATP-citrate lyase in complex with inhi... -

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Basic information

Entry
Database: EMDB / ID: EMD-0567
TitleCryo-EM structure of human ATP-citrate lyase in complex with inhibitor NDI-091143
Map dataem-volume_P1
Sample
  • Complex: protein-inhibitor complex
    • Protein or peptide: ATP-citrate synthase
  • Ligand: methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl)sulfamoyl]-4-hydroxybenzoate
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsATP-citrate lyase / LIGASE / ligase-ligase inhibitor complex
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
ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsWei J / Tong L
Funding support United States, 4 items
OrganizationGrant numberCountry
Other privateNimbus Therapeutics United States
Other privateSimons Foundation (349247) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other governmentNYSTAR United States
CitationJournal: Nature / Year: 2019
Title: An allosteric mechanism for potent inhibition of human ATP-citrate lyase.
Authors: Jia Wei / Silvana Leit / Jun Kuai / Eric Therrien / Salma Rafi / H James Harwood / Byron DeLaBarre / Liang Tong /
Abstract: ATP-citrate lyase (ACLY) is a central metabolic enzyme and catalyses the ATP-dependent conversion of citrate and coenzyme A (CoA) to oxaloacetate and acetyl-CoA. The acetyl-CoA product is crucial for ...ATP-citrate lyase (ACLY) is a central metabolic enzyme and catalyses the ATP-dependent conversion of citrate and coenzyme A (CoA) to oxaloacetate and acetyl-CoA. The acetyl-CoA product is crucial for the metabolism of fatty acids, the biosynthesis of cholesterol, and the acetylation and prenylation of proteins. There has been considerable interest in ACLY as a target for anti-cancer drugs, because many cancer cells depend on its activity for proliferation. ACLY is also a target against dyslipidaemia and hepatic steatosis, with a compound currently in phase 3 clinical trials. Many inhibitors of ACLY have been reported, but most of them have weak activity. Here we report the development of a series of low nanomolar, small-molecule inhibitors of human ACLY. We have also determined the structure of the full-length human ACLY homo-tetramer in complex with one of these inhibitors (NDI-091143) by cryo-electron microscopy, which reveals an unexpected mechanism of inhibition. The compound is located in an allosteric, mostly hydrophobic cavity next to the citrate-binding site, and requires extensive conformational changes in the enzyme that indirectly disrupt citrate binding. The observed binding mode is supported by and explains the structure-activity relationships of these compounds. This allosteric site greatly enhances the 'druggability' of ACLY and represents an attractive target for the development of new ACLY inhibitors.
History
DepositionFeb 16, 2019-
Header (metadata) releaseMar 13, 2019-
Map releaseApr 17, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6o0h
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0567.png

Downloads & links

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Map

FileDownload / File: emd_0567.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem-volume_P1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.488 Å		1.06 Å/pix.
x 256 pix.
= 271.488 Å		1.06 Å/pix.
x 256 pix.
= 271.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0605 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021 / Movie #1: 0.021
Minimum - Maximum-0.071151875 - 0.13068005
Average (Standard dev.)0.0003900957 (±0.0040762406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.488 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06051.06051.0605
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.488271.488271.488
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0710.1310.000

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Supplemental data

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Mask #1

Fileemd_0567_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: em-half-volume P1

Fileemd_0567_half_map_1.map
Annotationem-half-volume_P1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: em-half-volume P2

Fileemd_0567_half_map_2.map
Annotationem-half-volume_P2
Projections & Slices
AxesZYX

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Sample components

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Entire : protein-inhibitor complex

EntireName: protein-inhibitor complex
Components
  • Complex: protein-inhibitor complex
    • Protein or peptide: ATP-citrate synthase
  • Ligand: methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl)sulfamoyl]-4-hydroxybenzoate
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: protein-inhibitor complex

SupramoleculeName: protein-inhibitor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP-citrate synthase

MacromoleculeName: ATP-citrate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ATP citrate synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.787102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAKAISEQT GKELLYKFIC TTSAIQNRFK YARVTPDTDW ARLLQDHPWL LSQNLVVKPD QLIKRRGKLG LVGVNLTLDG VKSWLKPRL GQEATVGKAT GFLKNFLIEP FVPHSQAEEF YVCIYATREG DYVLFHHEGG VDVGDVDAKA QKLLVGVDEK L NPEDIKKH ...String:
MSAKAISEQT GKELLYKFIC TTSAIQNRFK YARVTPDTDW ARLLQDHPWL LSQNLVVKPD QLIKRRGKLG LVGVNLTLDG VKSWLKPRL GQEATVGKAT GFLKNFLIEP FVPHSQAEEF YVCIYATREG DYVLFHHEGG VDVGDVDAKA QKLLVGVDEK L NPEDIKKH LLVHAPEDKK EILASFISGL FNFYEDLYFT YLEINPLVVT KDGVYVLDLA AKVDATADYI CKVKWGDIEF PP PFGREAY PEEAYIADLD AKSGASLKLT LLNPKGRIWT MVAGGGASVV YSDTICDLGG VNELANYGEY SGAPSEQQTY DYA KTILSL MTREKHPDGK ILIIGGSIAN FTNVAATFKG IVRAIRDYQG PLKEHEVTIF VRRGGPNYQE GLRVMGEVGK TTGI PIHVF GTETHMTAIV GMALGHRPIP NQPPTAAHTA NFLLNASGST STPAPSRTAS FSESRADEVA PAKKAKPAMP QDSVP SPRS LQGKSTTLFS RHTKAIVWGM QTRAVQGMLD FDYVCSRDEP SVAAMVYPFT GDHKQKFYWG HKEILIPVFK NMADAM RKH PEVDVLINFA SLRSAYDSTM ETMNYAQIRT IAIIAEGIPE ALTRKLIKKA DQKGVTIIGP ATVGGIKPGC FKIGNTG GM LDNILASKLY RPGSVAYVSR SGGMSNELNN IISRTTDGVY EGVAIGGDRY PGSTFMDHVL RYQDTPGVKM IVVLGEIG G TEEYKICRGI KEGRLTKPIV CWCIGTCATM FSSEVQFGHA GACANQASET AVAKNQALKE AGVFVPRSFD ELGEIIQSV YEDLVANGVI VPAQEVPPPT VPMDYSWARE LGLIRKPASF MTSICDERGQ ELIYAGMPIT EVFKEEMGIG GVLGLLWFQK RLPKYSCQF IEMCLMVTAD HGPAVSGAHN TIICARAGKD LVSSLTSGLL TIGDRFGGAL DAAAKMFSKA FDSGIIPMEF V NKMKKEGK LIMGIGHRVK SINNPDMRVQ ILKDYVRQHF PATPLLDYAL EVEKITTSKK PNLILNVDGL IGVAFVDMLR NC GSFTREE ADEYIDIGAL NGIFVLGRSM GFIGHYLDQK RLKQGLYRHP WDDISYVLPE HMSMKLAAAL EHHHHHHHH

UniProtKB: ATP-citrate synthase

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Macromolecule #2: methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl)sulfamoyl]-4...

MacromoleculeName: methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl)sulfamoyl]-4-hydroxybenzoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: LBG
Molecular weightTheoretical: 453.844 Da
Chemical component information

ChemComp-LBG:
methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl)sulfamoyl]-4-hydroxybenzoate

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
300.0 mMNaClSodium chloride
2.0 mMDTTDithiothreitol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2803 / Average exposure time: 10.0 sec. / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 250156
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 11452
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta-2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta-2)
Final 3D classificationSoftware - Name: RELION (ver. 3.0-beta-2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6o0h:
Cryo-EM structure of human ATP-citrate lyase in complex with inhibitor NDI-091143

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