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- EMDB-43362: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H... -

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Basic information

Entry
Database: EMDB / ID: EMD-43362
TitlePRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H3 tail disengaged
Map data
Sample
  • Complex: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Histone-lysine N-methyltransferase EZH2
    • Protein or peptide: Protein Jumonji
    • Protein or peptide: Isoform 3 of Zinc finger protein AEBP2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
Keywordscomplex / methyltransferase / histone / epigenetics / GENE REGULATION
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / CAF-1 complex / negative regulation of keratinocyte differentiation ...protein localization to pericentric heterochromatin / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / CAF-1 complex / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / primary miRNA binding / random inactivation of X chromosome / regulation of adaxial/abaxial pattern formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / regulatory ncRNA-mediated heterochromatin formation / negative regulation of cardiac muscle cell proliferation / histone H3K27 methyltransferase activity / sex chromatin / ubiquitin-modified histone reader activity / positive regulation of cell cycle G1/S phase transition / NURF complex / facultative heterochromatin formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / genomic imprinting / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / negative regulation of stem cell differentiation / regulation of stem cell differentiation / RSC-type complex / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / cardiac muscle hypertrophy in response to stress / chromatin silencing complex / histone H3K9me2/3 reader activity / Transcription of E2F targets under negative control by DREAM complex / pronucleus / positive regulation of dendrite development / G1 to G0 transition / histone H3 methyltransferase activity / histone methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / ATPase complex / lncRNA binding / negative regulation of gene expression, epigenetic / synaptic transmission, GABAergic / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / : / positive regulation of stem cell population maintenance / positive regulation of MAP kinase activity / histone methyltransferase complex / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of transcription elongation by RNA polymerase II / G0 and Early G1 / positive regulation of GTPase activity / positive regulation of protein serine/threonine kinase activity / negative regulation of cell differentiation / cardiac muscle cell proliferation / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / subtelomeric heterochromatin formation / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / nucleosome binding / keratinocyte differentiation / spleen development / Regulation of TP53 Activity through Acetylation / protein localization to chromatin / liver regeneration / negative regulation of cytokine production involved in inflammatory response / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / SUMOylation of chromatin organization proteins / thymus development / cellular response to leukemia inhibitory factor / central nervous system development / B cell differentiation / ubiquitin binding / Regulation of PTEN gene transcription / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / transcription coregulator activity / hippocampus development
Similarity search - Function
: / Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 ...: / Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / : / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / JmjC domain, hydroxylase / SET domain / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Polycomb protein EED / Histone-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Zinc finger protein AEBP2 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCookis T / Nogales E
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127018 United States
National Science Foundation (NSF, United States)GM-08295 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications.
Authors: Trinity Cookis / Alexandria Lydecker / Paul Sauer / Vignesh Kasinath / Eva Nogales /
Abstract: Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is ...Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is regulated by protein cofactors and their crosstalk with histone modifications. Trimethylated histone H3 on K4 (H3K4me3) and K36 (H3K36me3) localize to sites of active transcription and inhibit PRC2 activity through unknown mechanisms. Using cryo-electron microscopy, we reveal that histone H3 tails containing H3K36me3 engage poorly with PRC2 and preclude its effective interaction with chromatin, while H3K4me3 binds to the allosteric site in the EED subunit, acting as an antagonist that competes with activators required for spreading of the H3K27me3 repressive mark. Thus, the location of the H3K4me3 and H3K36me3 modifications along the H3 tail allows them to target two requirements for efficient trimethylation of H3K27 by PRC2. We further show that the JARID2 cofactor modulates PRC2 activity in the presence of these histone modifications.
History
DepositionJan 14, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43362.png

Downloads & links

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Map

FileDownload / File: emd_43362.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.288
Minimum - Maximum-0.51080847 - 1.2538651
Average (Standard dev.)0.00045936296 (±0.03735113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43362_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43362_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : PRC2_AJ1-450 bound to H3K36me3-modified nucleosome

EntireName: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome
Components
  • Complex: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Histone-lysine N-methyltransferase EZH2
    • Protein or peptide: Protein Jumonji
    • Protein or peptide: Isoform 3 of Zinc finger protein AEBP2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome

SupramoleculeName: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.181922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN ...String:
MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN DKPSPNSENE QNSVTLEVLL VKVCHKKRKD VSCPIRQVPT GKKQVPLNPD LNQTKPGNFP SLAVSSNEFE PS NSHMVKS YSLLFRVTRP GRREFNGMIN GETNENIDVN EELPARRKRN REDGEKTFVA QMTVFDKNRR LQLLDGEYEV AMQ EMEECP ISKKRATWET ILDGKRLPPF ETFSQGPTLQ FTLRWTGETN DKSTAPIAKP LATRNSESLH QENKPGSVKP TQTI AVKES LTTDLQTRKE KDTPNENRQK LRIFYQFLYN NNTRQQTEAR DDLHCPWCTL NCRKLYSLLK HLKLCHSRFI FNYVY HPKG ARIDVSINEC YDGSYAGNPQ DIHRQPGFAF SRNGPVKRTP ITHILVCRPK RTKASMSEFL ESEDGEVEQQ RTYSSG HNR LYFHSDTCLP LRPQEMEVDS EDEKDPEWLR EKTITQIEEF SDVNEGEKEV MKLWNLHVMK HGFIADNQMN HACMLFV EN YGQKIIKKNL CRNFMLHLVS MHDFNLISIM SIDKAVTKLR EMQQKLEKGE SASPANEEIT EEQNGTANGF SEINSKEK A LETDSVSGVS KQSKKQKL

UniProtKB: Polycomb protein SUZ12

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Macromolecule #2: Polycomb protein EED

MacromoleculeName: Polycomb protein EED / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.267691 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS ...String:
MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS RGIIRIINPI TMQCIKHYVG HGNAINELKF HPRDPNLLLS VSKDHALRLW NIQTDTLVAI FGGVEGHRDE VL SADYDLL GEKIMSCGMD HSLKLWRINS KRMMNAIKES YDYNPNKTNR PFISQKIHFP DFSTRDIHRN YVDCVRWLGD LIL SKSCEN AIVCWKPGKM EDDIDKIKPS ESNVTILGRF DYSQCDIWYM RFSMDFWQKM LALGNQVGKL YVWDLEVEDP HKAK CTTLT HHKCGAAIRQ TSFSRDSSIL IAVCDDASIW RWDRLR

UniProtKB: Polycomb protein EED

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Macromolecule #3: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String:
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS

UniProtKB: Histone-binding protein RBBP4

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Macromolecule #4: Histone-lysine N-methyltransferase EZH2

MacromoleculeName: Histone-lysine N-methyltransferase EZH2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine27 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.492297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVHI LTSVSSLRGT RECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN FMVEDETVLH NIPYMGDEVL DQDGTFIEEL IKNYDGKVHG D RECGFIND ...String:
MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVHI LTSVSSLRGT RECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN FMVEDETVLH NIPYMGDEVL DQDGTFIEEL IKNYDGKVHG D RECGFIND EIFVELVNAL GQYNDDDDDD DGDDPEEREE KQKDLEDHRD DKESRPPRKF PSDKIFEAIS SMFPDKGTAE EL KEKYKEL TEQQLPGALP PECTPNIDGP NAKSVQREQS LHSFHTLFCR RCFKYDCFLH PFHATPNTYK RKNTETALDN KPC GPQCYQ HLEGAKEFAA ALTAERIKTP PKRPGGRRRG RLPNNSSRPS TPTINVLESK DTDSDREAGT ETGGENNDKE EEEK KDETS SSSEANSRCQ TPIKMKPNIE PPENVEWSGA EASMFRVLIG TYYDNFCAIA RLIGTKTCRQ VYEFRVKESS IIAPA PAED VDTPPRKKKR KHRLWAAHCR KIQLKKDGSS NHVYNYQPCD HPRQPCDSSC PCVIAQNFCE KFCQCSSECQ NRFPGC RCK AQCNTKQCPC YLAVRECDPD LCLTCGAADH WDSKNVSCKN CSIQRGSKKH LLLAPSDVAG WGIFIKDPVQ KNEFISE YC GEIISQDEAD RRGKVYDKYM CSFLFNLNND FVVDATRKGN KIRFANHSVN PNCYAKVMMV NGDHRIGIFA KRAIQTGE E LFFDYRYSQA DALKYVGIER EMEIP

UniProtKB: Histone-lysine N-methyltransferase EZH2

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Macromolecule #5: Protein Jumonji

MacromoleculeName: Protein Jumonji / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.174879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SKERPKRNII QKKYDDSDGI PWSEERVVRK VLYLSLKEFK NSQKRQHAEG IAGSLKTVNG LLGNDQSKGL GPASEQSENE KDDASQVSS TSNDVSSSDF EEGPSRKRPR LQAQR(M3L)FAQS QPNSPSTTPV KIVEPLLPPP ATQISDLSKR KPKTEDF LT FLCLRGSPAL ...String:
SKERPKRNII QKKYDDSDGI PWSEERVVRK VLYLSLKEFK NSQKRQHAEG IAGSLKTVNG LLGNDQSKGL GPASEQSENE KDDASQVSS TSNDVSSSDF EEGPSRKRPR LQAQR(M3L)FAQS QPNSPSTTPV KIVEPLLPPP ATQISDLSKR KPKTEDF LT FLCLRGSPAL PNSMVYFGSS QDEEEVEEED DETEDVKTAT NNASSSCQST PRKGKTHKHV HNGHVFNGSS RSTREKEP V QKHKSKEATP AKEKHSDHRA DSRREQASAN HPAAAPSTGS SAKGLAATHH HPPLHRSAQD LRKQVSKVNG VTRMSSLGA GVTSAKKMRE VRPSPSKTVK YTATVTKGAV TYTKAKRELV KDTKPNHHKP SSAVNHTISG KTESSNAKTR KQVLSLGGAS KSTGPAVNG LKVSGRLNPK SCTKEVGGRQ LREGLQLREG LRNSKRRLEE AHQA

UniProtKB: Protein Jumonji

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Macromolecule #6: Isoform 3 of Zinc finger protein AEBP2

MacromoleculeName: Isoform 3 of Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.042133 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYTRRYSSIS STIMDVDSTI SSGRSTPAMM NGQGSTTSSS KNIAYNCCWD QCQACFNSSP DLADHIRSIH VDGQRGGVFV CLWKGCKVY NTPSTSQSWL QRHMLTHSGD KPFKCVVGGC NASFASQGGL ARHVPTHFSQ QNSSKVSSQP KAKEESPSKA G MNKRRKLK ...String:
MYTRRYSSIS STIMDVDSTI SSGRSTPAMM NGQGSTTSSS KNIAYNCCWD QCQACFNSSP DLADHIRSIH VDGQRGGVFV CLWKGCKVY NTPSTSQSWL QRHMLTHSGD KPFKCVVGGC NASFASQGGL ARHVPTHFSQ QNSSKVSSQP KAKEESPSKA G MNKRRKLK NKRRRSLPRP HDFFDAQTLD AIRHRAICFN LSAHIESLGK GHSVVFHSTV IAKRKEDSGK IKLLLHWMPE DI LPDVWVN ESERHQLKTK VVHLSKLPKD TALLLDPNIY RTMPQKRLKR TLIRKVFNLY LSKQ

UniProtKB: Zinc finger protein AEBP2

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Macromolecule #7: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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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

Concentration0.28 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

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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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

21707

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44519
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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