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- EMDB-76027: Antibody (1B2) Bound Rifamycin Synthetase Module 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-76027
TitleAntibody (1B2) Bound Rifamycin Synthetase Module 2
Map dataAntibody (1B2) Bound Rifamycin Synthetase Module 2
Sample
  • Complex: rifamycin synthetase module 2 in complex with antibody fragment 1B2
    • Protein or peptide: 6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2
    • Protein or peptide: 1B2 Antibody Fragment (Fab) Heavy Chain
    • Protein or peptide: 1B2 Antibody Fragment (Fab) Light Chain
Keywordspolyketide synthase / antibody / BIOSYNTHETIC PROTEIN-Immune System complex
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Erythronolide synthase, docking / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase ...Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Erythronolide synthase, docking / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / ANL, N-terminal domain / : / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / AMP-binding, conserved site / Putative AMP-binding domain signature. / Acyl transferase domain superfamily / : / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / AMP-binding enzyme, C-terminal domain superfamily / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase / Erythronolide synthase EryA2
Similarity search - Component
Biological speciesAmycolatopsis mediterranei (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsCogan DP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM160153 United States
CitationJournal: To Be Published
Title: Antibody (1B2) Bound Rifamycin Synthetase Module 2
Authors: Cogan DP
History
DepositionMar 11, 2026-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76027.png

Downloads & links

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Map

FileDownload / File: emd_76027.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody (1B2) Bound Rifamycin Synthetase Module 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 448 pix.
= 492.8 Å		1.1 Å/pix.
x 448 pix.
= 492.8 Å		1.1 Å/pix.
x 448 pix.
= 492.8 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: 0.235
Minimum - Maximum-0.27485472 - 0.9546542
Average (Standard dev.)-0.00011771698 (±0.013643485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 492.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_76027_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_76027_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rifamycin synthetase module 2 in complex with antibody fragment 1B2

EntireName: rifamycin synthetase module 2 in complex with antibody fragment 1B2
Components
  • Complex: rifamycin synthetase module 2 in complex with antibody fragment 1B2
    • Protein or peptide: 6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2
    • Protein or peptide: 1B2 Antibody Fragment (Fab) Heavy Chain
    • Protein or peptide: 1B2 Antibody Fragment (Fab) Light Chain

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Supramolecule #1: rifamycin synthetase module 2 in complex with antibody fragment 1B2

SupramoleculeName: rifamycin synthetase module 2 in complex with antibody fragment 1B2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Amycolatopsis mediterranei (bacteria)
Molecular weightTheoretical: 335.62681 kDa/nm

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Macromolecule #1: 6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2

MacromoleculeName: 6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Amycolatopsis mediterranei (bacteria)
Molecular weightTheoretical: 115.872844 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL EEEPIAIVAM ACRFPGGVHS PEDLWRLVAD GADAVTEFPA DRGWDTDRLY HEDPDHEGT TYVRHGAFLD DAAGFDAAFF GISPNEALAM DPQQRLLLET SWELFERAAI DPTTLAGQDI GVFAGVNSHD Y SMRMHRAA ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL EEEPIAIVAM ACRFPGGVHS PEDLWRLVAD GADAVTEFPA DRGWDTDRLY HEDPDHEGT TYVRHGAFLD DAAGFDAAFF GISPNEALAM DPQQRLLLET SWELFERAAI DPTTLAGQDI GVFAGVNSHD Y SMRMHRAA GVEGFRLTGG SASVLSGRVA YHFGVEGPAV TVDTACSSSL VALHMAVQAL QRGECSMALA GGVMVMGTVE TF VEFSRQR GLAPDGRCKA FADGADGTGW SEGVGLLLVE RLSEAQRRGH QVLAVVRGSA VNSDGASNGL TAPNGPSQQR VIR KALAAA GLSTSDVDAV EAHGTGTTLG DPIEAEALLA TYGQNRETPL WLGSVKSNLG HTQAAAGVAG VIKMVMAMRH GVLP RTLHV DRPSSYVDWS AGAVELLTEA RDWVSNGHPR RAGVSSFGIG GTNAHVVLEE VAAPITTPQP EPAEFLVPVL VSART AAGL RGQAGRLAAF LGDRTDVRVP DAAYALATTR AQLDHRAVVL ASDRAQLCAD LAAFGSGVVT GTPVDGKLAV LFTGQG SQW AGMGRELAET FPVFRDAFEA ACEAVDTHLR ERPLREVVFD DSALLDQTMY TQGALFAVET ALFRLFESWG VRPGLLA GH SIGELAAAHV SGVLDLADAG ELVAARGRLM QALPAGGAMV AVQATEDEVA PLLDGTVCVA AVNGPDSVVL SGTEAAVL A VADELAGRGR KTRRLAVSHA FHSPLMEPML DDFRAVAERL TYRAGSLPVV STLTGELAAL DSPDYWVGQV RNAVRFSDA VTALGAQGAS TFLELGPGGA LAAMALGTLG GPEQSCVATL RKNGAEVPDV LTALAELHVR GVGVDWTTVL DEPATAVGTV LPTYAFQHQ RFWVDVDETA AVSVTPPPAE PIVDRPVQDV LELVRESAAV VLGHRDAGSF DLDRSFKDHG FDSLSAVKLR N RLRDFTGV ELPSTLIFDY PNPAVLADHL RAELLGEFAA SPAVDIGDRL DELEKALEAL SAEDGHDDVG QRLESLLRRW NS RRADAPS TSAISEDASD DELFSMLDQR FGGGEDLGNS SSVDKLAAAL EHHHHHH

UniProtKB: 6-deoxyerythronolide-B synthase, Erythronolide synthase EryA2

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Macromolecule #2: 1B2 Antibody Fragment (Fab) Heavy Chain

MacromoleculeName: 1B2 Antibody Fragment (Fab) 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: 1B2 Antibody Fragment (Fab) Light Chain

MacromoleculeName: 1B2 Antibody Fragment (Fab) 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

Concentration10 mg/mL
BufferpH: 7.2 / Component:
ConcentrationName
0.01 MHEPES
0.1 Mcitric acid
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.988 µm / Nominal defocus min: 1.188 µm
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

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 852885
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)

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