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- EMDB-41306: Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-41306
TitleCrosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in complex with antibody fragment 1B2: Crosslinked Intra-State 1
Map data
Sample
  • Complex: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2
    • Protein or peptide: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
    • Protein or peptide: Antibody Fragment 1B2, Heavy Chain
    • Protein or peptide: Antibody Fragment 1B2, Light Chain
Keywordspolyketide synthase / antibody / BIOSYNTHETIC PROTEIN-IMMUNE SYSTEM complex
Biological speciesSaccharopolyspora erythraea (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsCogan DP / Soohoo AM / Chen M / Brodsky KL / Liu Y / Khosla C
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141799 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129541 United States
National Science Foundation (NSF, United States)DGE-1656518 United States
CitationJournal: To Be Published
Title: Structural Basis for Intermodular Communication in Assembly-Line Polyketide Biosynthesis
Authors: Cogan DP / Soohoo AM / Chen M / Liu Y / Brodsky KL / Khosla C
History
DepositionJul 23, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41306.png

Downloads & links

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Map

FileDownload / File: emd_41306.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.416
Minimum - Maximum-0.36579013 - 1.461955
Average (Standard dev.)0.0007318131 (±0.029021468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41306_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41306_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2

EntireName: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2
Components
  • Complex: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2
    • Protein or peptide: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
    • Protein or peptide: Antibody Fragment 1B2, Heavy Chain
    • Protein or peptide: Antibody Fragment 1B2, Light Chain

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Supramolecule #1: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2

SupramoleculeName: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6

MacromoleculeName: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 188.891219 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPVAVVAM ACRLPGGVST PEEFWELLSE GRDAVAGLPT DRGWDLDSLF HPDPTRSGT AHQRGGGFLT EATAFDPAFF GMSPREALAV DPQQRLMLEL SWEVLERAGI PPTSLQASPT GVFVGLIPQE Y GPRLAEGG ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPVAVVAM ACRLPGGVST PEEFWELLSE GRDAVAGLPT DRGWDLDSLF HPDPTRSGT AHQRGGGFLT EATAFDPAFF GMSPREALAV DPQQRLMLEL SWEVLERAGI PPTSLQASPT GVFVGLIPQE Y GPRLAEGG EGVEGYLMTG TTTSVASGRI AYTLGLEGPA ISVDTACSSS LVAVHLACQS LRRGESSLAM AGGVTVMPTP GM LVDFSRM NSLAPDGRCK AFSAGANGFG MAEGAGMLLL ERLSDARRNG HPVLAVLRGT AVNSDGASNG LSAPNGRAQV RVI QQALAE SGLGPADIDA VEAHGTGTRL GDPIEARALF EAYGRDREQP LHLGSVKSNL GHTQAAAGVA GVIKMVLAMR AGTL PRTLH ASERSKEIDW SSGAISLLDE PEPWPAGARP RRAGVSSFGI SGTNAHAIIE EAPQVVEGER VEAGDVVAPW VLSAS SAEG LRAQAARLAA HLREHPGQDP RDIAYSLATG RAALPHRAAF APVDESAALR VLDGLATGNA DGAAVGTSRA QQRAVF VFP GQGWQWAGMA VDLLDTSPVF AAALRECADA LEPHLDFEVI PFLRAEAARR EQDAALSTER VDVVQPVMFA VMVSLAS MW RAHGVEPAAV IGHSQGEIAA ACVAGALSLD DAARVVALRS RVIATMPGNK GMASIAAPAG EVRARIGDRV EIAAVNGP R SVVVAGDSDE LDRLVASCTT ECIRAKRLAV DYASHSSHVE TIRDALHAEL GEDFHPLPGF VPFFSTVTGR WTQPDELDA GYWYRNLRRT VRFADAVRAL AEQGYRTFLE VSAHPILTAA IEEIGDGSGA DLSAIHSLRR GDGSLADFGE ALSRAFAAGV AVDWESVHL GTGARRVPLP TYPFQRERVW LEPKPVARRS TEVDEVSALR YRIEWRPTGA GEPARLDGTW LVAKYAGTAD E TSTAAREA LESAGARVRE LVVDARCGRD ELAERLRSVG EVAGVLSLLA VDEAEPEEAP LALASLADTL SLVQAMVSAE LG CPLWTVT ESAVATGPFE RVRNAAHGAL WGVGRVIALE NPAVWGGLVD VPAGSVAELA RHLAAVVSGG AGEDQLALRA DGV YGRRWV RAAAPATDDE WKPTGTVLVT GGTGGVGGQI ARWLARRGAP HLLLVSRSGP DADGAGELVA ELEALGARTT VAAC DVTDR ESVRELLGGI GDDVPLSAVF HAAATLDDGT VDTLTGERIE RASRAKVLGA RNLHELTREL DLTAFVLFSS FASAF GAPG LGGYAPGNAY LDGLAQQRRS DGLPATAVAW GTWAGSGMAE GPVADRFRRH GVIEMPPETA CRALQNALDR AEVCPI VID VRWDRFLLAY TAQRPTRLFD EIDDARRAAP QAAAEPRVGA LASLPAPERE KALFELVRSH AAAVLGHASA ERVPADQ AF AELGVD(4HH)LSA LELRNRLGAA TGVRLPTTTV FDHPDVRTLA AHLTSELGSG TPAREASSAL RDGYRQAGVS GRVR SYLDL LAGLSDFREH FDGSDGFSLD LVDMADGPGE VTVICCAGTA AISGPHEFTR LAGALRGIAP VRAVPQPGYE EGEPL PSSM AAVAAVQADA VIRTQGDKPF VVAGHSAGAL MAYALATELL DRGHPPRGVV LIDVYPPGHQ DAMNAWLEEL TATLFD RET VRMDDTRLTA LGAYDRLTGQ WRPRETGLPT LLVSAGEPMG PWPDDSWKPT WPFEHDTVAV PGDHFTMVQE HADAIAR HI DAWLGGGNSS SVDKLAAALE HHHHHH

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Macromolecule #2: Antibody Fragment 1B2, Heavy Chain

MacromoleculeName: Antibody Fragment 1B2, Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.447611 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEVQLVQSG GGLVQPGRSL RLSCTASGFT FGDYAMSWVR QAPGKGLEWV GFIRSKAYGG TTEYAASVKG RFTISRDDSK SIAYLQMNS LKTEDTAVYY CTRGGTLFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
MAEVQLVQSG GGLVQPGRSL RLSCTASGFT FGDYAMSWVR QAPGKGLEWV GFIRSKAYGG TTEYAASVKG RFTISRDDSK SIAYLQMNS LKTEDTAVYY CTRGGTLFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCAALVP RGSAHHHHHH AA DYKDDDD KA

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Macromolecule #3: Antibody Fragment 1B2, Light Chain

MacromoleculeName: Antibody Fragment 1B2, Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.715832 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQSLLHSNG YNYLDWYLQK PGQSPQLLIY LGSNRASGVP DRFSGSGSG TDFTLKISRV EAEDVGVYYC MQSLQTPRLT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPRGAKV ...String:
LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQSLLHSNG YNYLDWYLQK PGQSPQLLIY LGSNRASGVP DRFSGSGSG TDFTLKISRV EAEDVGVYYC MQSLQTPRLT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPRGAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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

Concentration8 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
100.0 mMC6H8O7citric acid
100.0 mMNaClsodium chloride
10.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9523 / Average exposure time: 3.76 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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: 434136
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92037
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 8 / Avg.num./class: 40000

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Atomic model buiding 1

Initial modelPDB ID:

7m7f


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8tjo:
Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in complex with antibody fragment 1B2: Crosslinked Intra-State 1

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