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- EMDB-53847: Cryo-EM structure of human ATP citrate lyase in complex with inhi... -

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Entry
Database: EMDB / ID: EMD-53847
TitleCryo-EM structure of human ATP citrate lyase in complex with inhibitor EVT0185-CoA
Map dataSharpened cryo-EM map following local refinement in combination with symmetry expansion (D2)
Sample
  • Complex: Human ATP citrate lyase (homotetramer)
    • Protein or peptide: Isoform 2 of ATP-citrate synthase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 6-[4-[6-[2-[3-[[4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-5,5-dimethyl-6-oxidanylidene-hexyl]phenyl]-2,2-dimethyl-hexanoic acid
KeywordsATP citrate lyase / ACL / ACLY / de novo lipogenesis / acetyl-CoA / citrate / oxaloacetate / cancer / LYASE
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 / fatty acid biosynthetic process / azurophil granule lumen / 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
ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsVerstraete K / Verschueren K / Savvides SN / Steinberg GR
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1524918N Belgium
CitationJournal: Nature / Year: 2025
Title: ACLY inhibition promotes tumour immunity and suppresses liver cancer.
Authors: Jaya Gautam / Jianhan Wu / James S V Lally / Jamie D McNicol / Russta Fayyazi / Elham Ahmadi / Daniela Carmen Oniciu / Spencer Heaton / Roger S Newton / Sonia Rehal / Dipankar Bhattacharya / ...Authors: Jaya Gautam / Jianhan Wu / James S V Lally / Jamie D McNicol / Russta Fayyazi / Elham Ahmadi / Daniela Carmen Oniciu / Spencer Heaton / Roger S Newton / Sonia Rehal / Dipankar Bhattacharya / Fiorella Di Pastena / Binh Nguyen / Celina M Valvano / Logan K Townsend / Suhrid Banskota / Battsetseg Batchuluun / Maria Joy Therese Jabile / Alice Payne / Junfeng Lu / Eric M Desjardins / Naoto Kubota / Evangelia E Tsakiridis / Bejal Mistry / Alex Aganostopoulos / Vanessa Houde / Ann Dansercoer / Koen H G Verschueren / Savvas N Savvides / Joanne A Hammill / Ksenia Bezverbnaya / Paola Muti / Theodoros Tsakiridis / Wenting Dai / Lei Jiang / Yujin Hoshida / Mark Larché / Jonathan L Bramson / Scott L Friedman / Kenneth Verstraete / Dongdong Wang / Gregory R Steinberg /
Abstract: Immunosuppressive tumour microenvironments are common in cancers such as metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma (HCC) (MASH-HCC). Although immune ...Immunosuppressive tumour microenvironments are common in cancers such as metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma (HCC) (MASH-HCC). Although immune cell metabolism influences effector function, the effect of tumour metabolism on immunogenicity is less understood. ATP citrate lyase (ACLY) links substrate availability and mitochondrial metabolism with lipid biosynthesis and gene regulation. Although ACLY inhibition shows antiproliferative effects in various tumours, clinical translation has been limited by challenges in inhibitor development and compensatory metabolic pathways. Here, using a mouse model of MASH-HCC that mirrors human disease, genetic inhibition of ACLY in hepatocytes and tumours reduced neoplastic lesions by over 70%. To evaluate the therapeutic potential of this pathway, a novel small-molecule ACLY inhibitor, EVT0185 (6-[4-(5-carboxy-5-methyl-hexyl)-phenyl]-2,2-dimethylhexanoic acid), was identified via phenotypic screening. EVT0185 is converted to a CoA thioester in the liver by SLC27A2 and structural analysis by cryo-electron microscopy reveals that EVT0185-CoA directly interacts with the CoA-binding site of ACLY. Oral delivery of EVT0185 in three mouse models of MASH-HCC dramatically reduces tumour burden as monotherapy and enhances efficacy of current standards of care including tyrosine kinase inhibitors and immunotherapies. Transcriptomic and spatial profiling in mice and humans linked reduced tumour ACLY with increases in the chemokine CXCL13, tumour-infiltrating B cells and tertiary lymphoid structures. The depletion of B cells blocked the antitumour effects of ACLY inhibition. Together, these findings illustrate how targeting tumour metabolism can rewire immune function and suppress cancer progression in MASH-HCC.
History
DepositionMay 18, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53847.png

Downloads & links

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Map

FileDownload / File: emd_53847.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map following local refinement in combination with symmetry expansion (D2)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 480 pix.
= 345.6 Å		0.72 Å/pix.
x 480 pix.
= 345.6 Å		0.72 Å/pix.
x 480 pix.
= 345.6 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
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Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5252451 - 0.8031328
Average (Standard dev.)-0.000004346402 (±0.017192211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53847_msk_1.map
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Additional map: Half-map B following non-uniform refinement in C1 symmetry

Fileemd_53847_additional_1.map
AnnotationHalf-map B following non-uniform refinement in C1 symmetry
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Additional map: Sharpened cryo-EM map in C1 symmetry

Fileemd_53847_additional_2.map
AnnotationSharpened cryo-EM map in C1 symmetry
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Additional map: Mask for FSC calculation in C1 symmetry

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Additional map: Non-sharpened cryo-EM map in C1 symmetry

Fileemd_53847_additional_4.map
AnnotationNon-sharpened cryo-EM map in C1 symmetry
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Additional map: Half-map A following non-uniform refinement in C1 symmetry

Fileemd_53847_additional_5.map
AnnotationHalf-map A following non-uniform refinement in C1 symmetry
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Additional map: Non-sharpened cryo-EM map following local refinement in combination...

Fileemd_53847_additional_6.map
AnnotationNon-sharpened cryo-EM map following local refinement in combination with symmetry expansion (D2)
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Additional map: Mask for FSC calculation following local refinement in...

Fileemd_53847_additional_7.map
AnnotationMask for FSC calculation following local refinement in combination with symmetry expansion (D2)
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Half map: Half-map A following local refinement in combination with...

Fileemd_53847_half_map_1.map
AnnotationHalf-map A following local refinement in combination with symmetry expansion (D2)
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Half map: Half-map B following local refinement in combination with...

Fileemd_53847_half_map_2.map
AnnotationHalf-map B following local refinement in combination with symmetry expansion (D2)
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Sample components

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Entire : Human ATP citrate lyase (homotetramer)

EntireName: Human ATP citrate lyase (homotetramer)
Components
  • Complex: Human ATP citrate lyase (homotetramer)
    • Protein or peptide: Isoform 2 of ATP-citrate synthase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 6-[4-[6-[2-[3-[[4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-5,5-dimethyl-6-oxidanylidene-hexyl]phenyl]-2,2-dimethyl-hexanoic acid

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Supramolecule #1: Human ATP citrate lyase (homotetramer)

SupramoleculeName: Human ATP citrate lyase (homotetramer) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Human ACLY was purified by IMAC and size-exclusion chromatography (SEC) using HiLoad 16/600 Superdex 200 and Superose 6 (Increase) columns with 20 mM HEPES, pH 7.4, 150 mM NaCl as a running ...Details: Human ACLY was purified by IMAC and size-exclusion chromatography (SEC) using HiLoad 16/600 Superdex 200 and Superose 6 (Increase) columns with 20 mM HEPES, pH 7.4, 150 mM NaCl as a running buffer. Top fractions from the final SEC elution peak were pooled and concentrated to 10 mg/mL, aliquoted, flash frozen and stored at -80 C freezer till further use.
Source (natural)Organism: Homo sapiens (human) / Location in cell: Cytoplasm
Molecular weightTheoretical: 486 KDa

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Macromolecule #1: Isoform 2 of ATP-citrate synthase

MacromoleculeName: Isoform 2 of ATP-citrate synthase / type: protein_or_peptide / ID: 1
Details: cDNA encoding full-length human ACLY (hACLY, Uniprot ID P53396-2) was prepared from poly A+ RNA from liver and cloned into the pTrcHis2 vector, in frame with a C-terminal Myc- and His-tag, ...Details: cDNA encoding full-length human ACLY (hACLY, Uniprot ID P53396-2) was prepared from poly A+ RNA from liver and cloned into the pTrcHis2 vector, in frame with a C-terminal Myc- and His-tag, resulting in pTrcHis2-hACLY (LMBP 11277). https://doi.org/10.1038/s41586-019-1095-5
Number of copies: 4 / Enantiomer: LEVO / EC number: ATP citrate synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.34257 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 QGKST TLFS RHTKAIVWGM QTRAVQGMLD FDYVCSRDEP SVAAMVYPFT GDHKQKFYWG HKEILIPVFK NMADAMRKHP EVDVLI NFA SLRSAYDSTM ETMNYAQIRT IAIIAEGIPE ALTRKLIKKA DQKGVTIIGP ATVGGIKPGC FKIGNTGGML DNILASK LY RPGSVAYVSR SGGMSNELNN IISRTTDGVY EGVAIGGDRY PGSTFMDHVL RYQDTPGVKM IVVLGEIGGT EEYKICRG I KEGRLTKPIV CWCIGTCATM FSSEVQFGHA GACANQASET AVAKNQALKE AGVFVPRSFD ELGEIIQSVY EDLVANGVI VPAQEVPPPT VPMDYSWARE LGLIRKPASF MTSICDERGQ ELIYAGMPIT EVFKEEMGIG GVLGLLWFQK RLPKYSCQFI EMCLMVTAD HGPAVSGAHN TIICARAGKD LVSSLTSGLL TIGDRFGGAL DAAAKMFSKA FDSGIIPMEF VNKMKKEGKL I MGIGHRVK SINNPDMRVQ ILKDYVRQHF PATPLLDYAL EVEKITTSKK PNLILNVDGL IGVAFVDMLR NCGSFTREEA DE YIDIGAL NGIFVLGRSM GFIGHYLDQK RLKQGLYRHP WDDISYVLPE HMSMKGEFEA YVEQKLISEE DLNSAVDHHH HHH

UniProtKB: ATP-citrate synthase

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #3: 6-[4-[6-[2-[3-[[4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-...

MacromoleculeName: 6-[4-[6-[2-[3-[[4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl- ...Name: 6-[4-[6-[2-[3-[[4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-5,5-dimethyl-6-oxidanylidene-hexyl]phenyl]-2,2-dimethyl-hexanoic acid
type: ligand / ID: 3 / Number of copies: 1 / Formula: W1K
Molecular weightTheoretical: 1.112022 KDa

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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

Concentration10 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.5 % (w/v)C32H58N2O8SCHAPSO
1.0 mMC10H16N5O13P3ATP
2.0 mMMgMg2+
4.0 mMC43H68N7O19P3SEVT0185-CoA

Details: HBS buffer supplemented with 0.5 % CHAPSO, 1 mM Mg2ATP and 4 mM EVT0185-CoA
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300
Details: Grids were glow discharged with a Pelco EasiGlOW instrument using a current of 15 mA for 10s at a pressure of 0.4 mBar.
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: Leica EM GP2.
DetailsThe sample was monodisperse. For cryo-EM grid preparation, purified ACLY (10 mg/mL in HBS buffer) was supplemented with 0.5 % CHAPSO, 1 mM Mg2ATP and 4 mM EVT0185-CoA.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7263 / Average electron dose: 61.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsMovies were processed via patch-based motion correction and CTF estimation as implemented in cryoSPARC v3.1.0.
Particle selectionNumber selected: 210900
Details: Initial high-resolution 2D classes were obtained via the Blob Picker job in cryoSPARC, followed by template-based picking and neural network-based particle picking via TOPAZ as implemented ...Details: Initial high-resolution 2D classes were obtained via the Blob Picker job in cryoSPARC, followed by template-based picking and neural network-based particle picking via TOPAZ as implemented in cryoSPARC. Ensuing 2D classification, 2D class selection and removal of potential duplicate particles within a distance of 150 Angstrom resulted in a particle set of 210,900 particles. Particles were extracted with a box size of 480 pixels with 2x binning.
CTF correctionSoftware - Name: cryoSPARC (ver. v3.1.0) / Software - details: patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.1.0) / Software - details: 3D Classification
Details: Following 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules ...Details: Following 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules (extracted from pdb 6xhx) were fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model.
Number images used: 280072
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.1.0) / Software - details: Ab initio
Details: Ab initio reconstruction in cryoSPARC (number of classes = 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.1.0) / Software - details: Local refinement / Details: Local refinement around one CCS arm and CCL module
Final 3D classificationNumber classes: 4 / Avg.num./class: 93000 / Software - Name: cryoSPARC (ver. v3.1.0) / Software - details: 3D Classification
Details: Refinement in C1 symmetry resulted in a pseudo-D2-symmetric cryo-EM volume with a golden-standard FSC0.143 resolution of 3.65 Angstrom that represented the ACLY tetramer. To possibly resolve ...Details: Refinement in C1 symmetry resulted in a pseudo-D2-symmetric cryo-EM volume with a golden-standard FSC0.143 resolution of 3.65 Angstrom that represented the ACLY tetramer. To possibly resolve the CCS-CCL assembly at higher resolution we applied symmetry expansion in combination with local refinement around one CCS arm and the central CCL module followed by 3D classification without alignment. 3 out of 4 classes were selected for the final reconstruction (total number of particles 280,072).
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6hxh


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsFollowing 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules (extracted from pdb 6xhx) were fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model. Cryo-EM map regions representing ligands in the ATP-grasp fold domain of the CCS module and in the CoA-binding domain were of the CSH module modelled as Mg.ADP and the adenosine 3'-phosphate 5'-diphosphate moiety of bound EVT0185-CoA, respectively. Restraints for EVT0185-CoA were generated via de Grade Web Server (https://grade.globalphasing.org).
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 138.8
Output model

PDB-9r90:
Cryo-EM structure of human ATP citrate lyase in complex with inhibitor EVT0185-CoA

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