[English] 日本語
Yorodumi
- EMDB-30434: Lovastatin nonaketide synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30434
TitleLovastatin nonaketide synthase
Map datalovB cryoEM map with C2 symmetry
Sample
  • Complex: Lovastatin nonaketide synthase
    • Protein or peptide: Lovastatin nonaketide synthase, polyketide synthase component
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function / homology
Function and homology information


malonyl-CoA metabolic process / lovastatin nonaketide synthase / lovastatin nonaketide synthase activity / lovastatin biosynthetic process / polyketide biosynthetic process / NADPH oxidation / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding ...malonyl-CoA metabolic process / lovastatin nonaketide synthase / lovastatin nonaketide synthase activity / lovastatin biosynthetic process / polyketide biosynthetic process / NADPH oxidation / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / methylation / oxidoreductase activity / ATP binding
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain ...Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Chloramphenicol acetyltransferase-like domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / Thiolase-like / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Lovastatin nonaketide synthase, polyketide synthase component
Similarity search - Component
Biological speciesAspergillus terreus (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsWang J / Wang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31470830 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the biosynthesis of lovastatin.
Authors: Jialiang Wang / Jingdan Liang / Lu Chen / Wei Zhang / Liangliang Kong / Chao Peng / Chen Su / Yi Tang / Zixin Deng / Zhijun Wang /
Abstract: Statins are effective cholesterol-lowering drugs. Lovastatin, one of the precursors of statins, is formed from dihydromonacolin L (DML), which is synthesized by lovastatin nonaketide synthase (LovB), ...Statins are effective cholesterol-lowering drugs. Lovastatin, one of the precursors of statins, is formed from dihydromonacolin L (DML), which is synthesized by lovastatin nonaketide synthase (LovB), with the assistance of a separate trans-acting enoyl reductase (LovC). A full DML synthesis comprises 8 polyketide synthetic cycles with about 35 steps. The assembling of the LovB-LovC complex, and the structural basis for the iterative and yet permutative functions of the megasynthase have remained a mystery. Here, we present the cryo-EM structures of the LovB-LovC complex at 3.60 Å and the core LovB at 2.91 Å resolution. The domain organization of LovB is an X-shaped face-to-face dimer containing eight connected domains. The binding of LovC laterally to the malonyl-acetyl transferase domain allows the completion of a L-shaped catalytic chamber consisting of six active domains. This architecture and the structural details of the megasynthase provide the basis for the processing of the intermediates by the individual catalytic domains. The detailed architectural model provides structural insights that may enable the re-engineering of the megasynthase for the generation of new statins.
History
DepositionAug 8, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateDec 15, 2021-
Current statusDec 15, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7cpx
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30434.png

Downloads & links

-
Map

FileDownload / File: emd_30434.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationlovB cryoEM map with C2 symmetry
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.0075 / Movie #1: 0.016
Minimum - Maximum-0.10426191 - 0.17728955
Average (Standard dev.)0.00017817336 (±0.0034254037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 350.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z350.000350.000350.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.1040.1770.000

-
Supplemental data

-
Half map: half map1

Fileemd_30434_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map2

Fileemd_30434_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lovastatin nonaketide synthase

EntireName: Lovastatin nonaketide synthase
Components
  • Complex: Lovastatin nonaketide synthase
    • Protein or peptide: Lovastatin nonaketide synthase, polyketide synthase component
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Supramolecule #1: Lovastatin nonaketide synthase

SupramoleculeName: Lovastatin nonaketide synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aspergillus terreus (mold)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightExperimental: 335 kDa/nm

-
Macromolecule #1: Lovastatin nonaketide synthase, polyketide synthase component

MacromoleculeName: Lovastatin nonaketide synthase, polyketide synthase component
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: lovastatin nonaketide synthase
Source (natural)Organism: Aspergillus terreus (mold)
Molecular weightTheoretical: 336.446656 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAQSMYPNEP IVVVGSGCRF PGDANTPSKL WELLQHPRDV QSRIPKERFD VDTFYHPDGK HHGRTNAPYA YVLQDDLGAF DAAFFNIQA GEAESMDPQH RLLLETVYEA VTNAGMRIQD LQGTSTAVYV GVMTHDYETV STRDLESIPT YSATGVAVSV A SNRISYFF ...String:
MAQSMYPNEP IVVVGSGCRF PGDANTPSKL WELLQHPRDV QSRIPKERFD VDTFYHPDGK HHGRTNAPYA YVLQDDLGAF DAAFFNIQA GEAESMDPQH RLLLETVYEA VTNAGMRIQD LQGTSTAVYV GVMTHDYETV STRDLESIPT YSATGVAVSV A SNRISYFF DWHGPSMTID TACSSSLVAV HLAVQQLRTG QSSMAIAAGA NLILGPMTFV LESKLSMLSP SGRSRMWDAG AD GYARGEA VCSVVLKTLS QALRDGDTIE CVIRETGVNQ DGRTTGITMP NHSAQEALIK ATYAQAGLDI TKAEDRCQFF EAH GTGTPA GDPQEAEAIA TAFFGHEQVA RSDGNERAPL FVGSAKTVVG HTEGTAGLAG LMKASFAVRH GVIPPNLLFD KISP RVAPF YKNLRIPTEA TQWPALPPGQ PRRASVNSFG FGGTNAHAII EEYMEPEQNQ LRVSNNEDCP PMTGVLSLPL VLSAK SQRS LKIMMEEMLQ FLQSHPEIHL HDLTWSLLRK RSVLPFRRAI VGHSHETIRR ALEDAIEDGI VSSDFTTEVR GQPSVL GIF TGQGAQWPGM LKNLIEASPY VRNIVRELDD SLQSLPEKYR PSWTLLDQFM LEGEASNVQY ATFSQPLCCA VQIVLVR LL EAARIRFTAV VGHSSGEIAC AFAAGLISAS LAIRIAYLRG VVSAGGARGT PGAMLAAGMS FEEAQEICEL DAFEGRIC V AASNSPDSVT FSGDANAIDH LKGMLEDEST FARLLKVDTA YHSHHMLPCA DPYMQALEEC GCAVADAGSP AGSVPWYSS VDAENRQMAA RDVTAKYWKD NLVSPVLFSH AVQRAVVTHK ALDIGIEVGC HPALKSPCVA TIKDVLSGVD LAYTGCLERG KNDLDSFSR ALAYLWERFG ASSFDADEFM RAVAPDRPCM SVSKLLPAYP WDRSRRYWVE SRATRHHLRG PKPHLLLGKL S EYSTPLSF QWLNFVRPRD IEWLDGHALQ GQTVFPAAGY IVMAMEAALM IAGTHAKQVK LLEILDMSID KAVIFDDEDS LV ELNLTAD VSRNAGEAGS MTISFKIDSC LSKEGNLSLS AKGQLALTIE DVNPRTTSAS DQHHLPPPEE EHPHMNRVNI NAF YHELGL MGYNYSKDFR RLHNMQRADL RASGTLDFIP LMDEGNGCPL LLHPASLDVA FQTVIGAYSS PGDRRLRCLY VPTH VDRIT LVPSLCLATA ESGCEKVAFN TINTYDKGDY LSGDIVVFDA EQTTLFQVEN ITFKPFSPPD ASTDHAMFAR WSWGP LTPD SLLDNPEYWA TAQDKEAIPI IERIVYFYIR SFLSQLTLEE RQQAAFHLQK QIEWLEQVLA SAKEGRHLWY DPGWEN DTE AQIEHLCTAN SYHPHVRLVQ RVGQHLLPTV RSNGNPFDLL DHDGLLTEFY TNTLSFGPAL HYARELVAQI AHRYQSM DI LEIGAGTGGA TKYVLATPQL GFNSYTYTDI STGFFEQARE QFAPFEDRMV FEPLDIRRSP AEQGFEPHAY DLIIASNV L HATPDLEKTM AHARSLLKPG GQMVILEITH KEHTRLGFIF GLFADWWAGV DDGRCTEPFV SFDRWDAILK RVGFSGVDS RTTDRDANLF PTSVFSTHAI DATVEYLDAP LASSGTVKDS YPPLVVVGGQ TPQSQRLLND IKAIMPPRPL QTYKRLVDLL DAEELPMKS TFVMLTELDE ELFAGLTEET FEATKLLLTY ASNTVWLTEN AWVQHPHQAS TIGMLRSIRR EHPDLGVHVL D VDAVETFD ATFLVEQVLR LEEHTDELAS STTWTQEPEV SWCKGRPWIP RLKRDLARNN RMNSSRRPIY EMIDSSRAPV AL QTARDSS SYFLESAETW FVPESVQQME TKTIYVHFSC PHALRVQALG FFYLVQGHVQ EGNREVPVVA LAERNASIVH VRP DYIYTE ADNNLSEGGG SLMVTVLAAA VLAETVISTA KCLGVTDSIL VLNPPSICGQ MLLHAGEEIG LQVHLATTSG NRSS VSAGD AKSWLTLHAR DTDWHLRRVL PRGVQALVDL SADQSCEGLT QRMMKVLMPG CAHYRAADLF TDTVSTELHS GSRHQ ASLP AAYWEHVVSL ARQGLPSVSE GWEVMPCTQF AAHADKTRPD LSTVISWPRE SDEATLPTRV RSIDAETLFA ADKTYL LVG LTGDLGRSLG RWMVQHGACH IVLTSRNPQV NPKWLAHVEE LGGRVTVLSM DVTSQNSVEA GLAKLKDLHL PPVGGIA FG PLVLQDVMLN NMELPMMEMV LNPKVEGVRI LHEKFSDPTS SNPLDFFVMF SSIVAVMGNP GQANYSAANC YLQALAQQ R VASGLAASTI DIGAVYGVGF VTRAELEEDF NAIRFMFDSV EEHELHTLFA EAVVAGRRAV HQQEQQRKFA TVLDMADLE LTTGIPPLDP ALKDRITFFD DPRIGNLKIP EYRGAKAGEG AAGSKGSVKE QLLQATNLDQ VRQIVIDGLS AKLQVTLQIP DGESVHPTI PLIDQGVDSL GAVTVGTWFS KQLYLDLPLL KVLGGASITD LANEAAARLP PSSIPLVAAT DGGAESTDNT S ENEVSGRE DTDLSAAATI TEPSSADEDD TEPGDEDVPR SHHPLSLGQE YSWRIQQGAE DPTVFNNTIG MFMKGSIDLK RL YKALRAV LRRHEIFRTG FANVDENGMA QLVFGQTKNK VQTIQVSDRA GAEEGYRQLV QTRYNPAAGD TLRLVDFFWG QDD HLLVVA YHRLVGDGST TENIFVEAGQ LYDGTSLSPH VPQFADLAAR QRAMLEDGRM EEDLAYWKKM HYRPSSIPVL PLMR PLVGN SSRSDTPNFQ HCGPWQQHEA VARLDPMVAF RIKERSRKHK ATPMQFYLAA YQVLLARLTD STDLTVGLAD TNRAT VDEM AAMGFFANLL PLRFRDFRPH ITFGEHLIAT RDLVREALQH ARVPYGVLLD QLGLEVPVPT SNQPAPLFQA VFDYKQ GQA ESGTIGGAKI TEVIATRERT PYDVVLEMSD DPTKDPLLTA KLQSSRYEAH HPQAFLESYM SLLSMFSMNP ALKLAHV HH HHHH

-
Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE
DetailsThis sample was homogenous

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 205047
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more