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- PDB-2vkz: Structure of the cerulenin-inhibited fungal fatty acid synthase t... -

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Basic information

Entry
Database: PDB / ID: 2vkz
TitleStructure of the cerulenin-inhibited fungal fatty acid synthase type I multienzyme complex
Components
  • FATTY ACID SYNTHASE SUBUNIT ALPHA
  • FATTY ACID SYNTHASE SUBUNIT BETA
KeywordsTRANSFERASE / PHOSPHORYLATION / PHOSPHOPANTETHEINE / FATTY ACID SYNTHASE / MULTIFUNCTIONAL ENZYME / OXIDOREDUCTASE / LIPID SYNTHESIS / FAS / NAD / NADP / LYASE / CERULENIN / HYDROLASE / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid synthase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #120 / Transcription Elongation Factor S-II; Chain A - #70 / Lipocalin - #700 / Arylsulfatase, C-terminal domain - #100 / Alpha-Beta Plaits - #3320 / Alpha-Beta Plaits - #3330 / Helix Hairpins - #1400 / Hydrophobic Seed Protein / Hydrophobic Seed Protein - #10 / : ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #120 / Transcription Elongation Factor S-II; Chain A - #70 / Lipocalin - #700 / Arylsulfatase, C-terminal domain - #100 / Alpha-Beta Plaits - #3320 / Alpha-Beta Plaits - #3330 / Helix Hairpins - #1400 / Hydrophobic Seed Protein / Hydrophobic Seed Protein - #10 / : / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / Arylsulfatase, C-terminal domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Transcription Elongation Factor S-II; Chain A / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Helix Hairpins / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Phosphopantetheine attachment site. / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Lipocalin / Helix non-globular / Special / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CER / FLAVIN MONONUCLEOTIDE / Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4 Å
AuthorsJohansson, P. / Wiltschi, B. / Kumari, P. / Kessler, B. / Vonrhein, C. / Vonck, J. / Oesterhelt, D. / Grininger, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Inhibition of the Fungal Fatty Acid Synthase Type I Multienzyme Complex.
Authors: Johansson, P. / Wiltschi, B. / Kumari, P. / Kessler, B. / Vonrhein, C. / Vonck, J. / Oesterhelt, D. / Grininger, M.
History
DepositionJan 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GE" AND "HE" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GE" AND "HE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID SYNTHASE SUBUNIT ALPHA
B: FATTY ACID SYNTHASE SUBUNIT ALPHA
C: FATTY ACID SYNTHASE SUBUNIT ALPHA
G: FATTY ACID SYNTHASE SUBUNIT BETA
H: FATTY ACID SYNTHASE SUBUNIT BETA
I: FATTY ACID SYNTHASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,310,41912
Polymers1,308,3746
Non-polymers2,0456
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50250 Å2
ΔGint-328.2 kcal/mol
Surface area571100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)231.900, 231.900, 756.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.009, -1, -0.003), (0.015, -0.003, 1), (-1, 0.009, 0.015)217.80899, -11.43496, 223.66127
2given(-0.006, 0.02, -1), (-1, -0.011, 0.006), (-0.011, 1, 0.02)225.42664, 215.48335, 10.50734
3given(-1), (0.021, 1), (-1, 0.021)217.1186, -12.5452, 223.891
4given(-0.0165, 0.0156, -1), (-1, -0.0211, 0.0161), (-0.0208, 1, 0.0159)226.7422, 215.409, 11.3748

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Components

#1: Protein FATTY ACID SYNTHASE SUBUNIT ALPHA / / FAS ALPHA CHAIN


Mass: 207184.422 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P19097, fatty-acyl-CoA synthase system, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein FATTY ACID SYNTHASE SUBUNIT BETA / / FAS BETA CHAIN


Mass: 228940.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P07149, fatty-acyl-CoA synthase system, oleoyl-[acyl-carrier-protein] hydrolase
#3: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN / Cerulenin


Mass: 225.284 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antifungal, antibiotic*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
Nonpolymer details(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE (CER): THE C9-C12 TRUNCATED CERULENIN WAS ...(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE (CER): THE C9-C12 TRUNCATED CERULENIN WAS COVALENTLY RESTRAINED TO ALPHA CHAIN C1305.

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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: 3.9 Å3/Da / Density % sol: 0.69 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.039
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 4→25 Å / Num. obs: 169821 / % possible obs: 98 % / Observed criterion σ(I): 1.4 / Redundancy: 3.2 % / Biso Wilson estimate: 130.07 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 7
Reflection shellResolution: 4→4.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / % possible all: 98

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Processing

Software
NameClassification
piratemodel building
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
SOLOMONphasing
piratephasing
DMphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 4→24.993 Å / SU ML: 0.62 / σ(F): 1.34 / Phase error: 26.37 / Stereochemistry target values: MLHL
Details: PHASE-RESTRAINED DOMAIN-WISE RIGID BODY REFINEMENT TO 4A USING THE 3.1A S.CEREVISIAE FAS-COMPLEX, PDB-CODE 2UV8. MKPEVEQELAHILLTELLAYQFASPVRWIETQDVFLKDFNTERVVEIGPSPTLAGMAQRT LKNKYESY
RfactorNum. reflection% reflection
Rfree0.2675 8547 5.06 %
Rwork0.2679 --
obs0.2679 168779 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89.498 Å2 / ksol: 0.274 e/Å3
Displacement parametersBiso mean: 164.19 Å2
Baniso -1Baniso -2Baniso -3
1--20.9783 Å2-0 Å20 Å2
2---20.9783 Å20 Å2
3---42.8159 Å2
Refinement stepCycle: LAST / Resolution: 4→24.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms85830 0 129 0 85959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187747
X-RAY DIFFRACTIONf_angle_d1.16118833
X-RAY DIFFRACTIONf_dihedral_angle_d18.5832262
X-RAY DIFFRACTIONf_chiral_restr0.0713323
X-RAY DIFFRACTIONf_plane_restr015333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.04530.38452540.38125248X-RAY DIFFRACTION97
4.0453-4.09270.38942480.37285335X-RAY DIFFRACTION98
4.0927-4.14240.34442890.36415378X-RAY DIFFRACTION98
4.1424-4.19450.39242880.3575280X-RAY DIFFRACTION98
4.1945-4.24950.31723210.34815323X-RAY DIFFRACTION98
4.2495-4.30740.3282940.335333X-RAY DIFFRACTION98
4.3074-4.36860.31852860.32515330X-RAY DIFFRACTION98
4.3686-4.43350.32843010.31625291X-RAY DIFFRACTION98
4.4335-4.50240.32472450.30955349X-RAY DIFFRACTION98
4.5024-4.57570.29672930.3015323X-RAY DIFFRACTION98
4.5757-4.65410.30152730.29475381X-RAY DIFFRACTION98
4.6541-4.73820.30153070.28785338X-RAY DIFFRACTION98
4.7382-4.82870.27932920.28775357X-RAY DIFFRACTION98
4.8287-4.92650.28522680.28365334X-RAY DIFFRACTION98
4.9265-5.03280.26122870.27835377X-RAY DIFFRACTION98
5.0328-5.14890.28862710.27825337X-RAY DIFFRACTION98
5.1489-5.27650.27582790.26835395X-RAY DIFFRACTION98
5.2765-5.41780.2562870.26575333X-RAY DIFFRACTION98
5.4178-5.57550.26733270.2675319X-RAY DIFFRACTION98
5.5755-5.75330.25512800.26845356X-RAY DIFFRACTION98
5.7533-5.95630.24922800.26415378X-RAY DIFFRACTION98
5.9563-6.19130.24682880.25735317X-RAY DIFFRACTION97
6.1913-6.46840.24433240.24475329X-RAY DIFFRACTION97
6.4684-6.80290.21572840.23685342X-RAY DIFFRACTION97
6.8029-7.21950.23732530.23065384X-RAY DIFFRACTION96
7.2195-7.76140.20642750.22575363X-RAY DIFFRACTION96
7.7614-8.51430.19832670.19745361X-RAY DIFFRACTION96
8.5143-9.68310.15362980.17345329X-RAY DIFFRACTION95
9.6831-11.97220.17523020.16985304X-RAY DIFFRACTION94
11.9722-24.99380.31112860.27745408X-RAY DIFFRACTION92

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