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- PDB-6ven: Yeast COMPASS in complex with a ubiquitinated nucleosome -

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Entry
Database: PDB / ID: 6ven
TitleYeast COMPASS in complex with a ubiquitinated nucleosome
Components
  • (601 DNA (146- ...) x 2
  • (COMPASS component ...) x 5
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-4 specific
  • Ubiquitin
KeywordsTRANSFERASE/STRUCTURAL PROTEIN/DNA / Methylation / histone / transcription / ubiquitin / gene regulation / TRANSFERASE-STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of synaptonemal complex assembly / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / sterol homeostasis / meiotic DNA double-strand break formation / [histone H3]-lysine4 N-trimethyltransferase / ascospore formation / synaptonemal complex assembly / regulation of chromatin organization ...positive regulation of synaptonemal complex assembly / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / sterol homeostasis / meiotic DNA double-strand break formation / [histone H3]-lysine4 N-trimethyltransferase / ascospore formation / synaptonemal complex assembly / regulation of chromatin organization / histone H3K4 trimethyltransferase activity / protein methylation / rDNA heterochromatin formation / Set1C/COMPASS complex / protein-lysine N-methyltransferase activity / RMTs methylate histone arginines / histone H3K4 methyltransferase activity / silent mating-type cassette heterochromatin formation / cellular response to stress / : / subtelomeric heterochromatin formation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / telomere maintenance / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling
Similarity search - Function
Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N ...Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Spp1/CFP1 / : / Dpy-30 motif / Dpy-30 motif / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Histone, subunit A / Histone, subunit A / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / : / Zinc finger, PHD-type / PHD zinc finger / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / WD domain, G-beta repeat / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / COMPASS component SWD3 / Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SWD1 ...S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / COMPASS component SWD3 / Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SWD1 / COMPASS component BRE2 / Histone H4 / Histone H3.2 / COMPASS component SPP1 / COMPASS component SDC1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Homo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWorden, E.J. / Wolberger, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130393 United States
CitationJournal: Elife / Year: 2020
Title: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome.
Authors: Evan J Worden / Xiangbin Zhang / Cynthia Wolberger /
Abstract: Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the ...Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxxxRR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: 601 DNA (146-MER)
J: 601 DNA (146-MER)
K: Ubiquitin
L: COMPASS component SWD3
M: COMPASS component SWD1
N: Histone-lysine N-methyltransferase, H3 lysine-4 specific
O: COMPASS component BRE2
P: COMPASS component SDC1
Q: COMPASS component SDC1
R: COMPASS component SPP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,46120
Polymers474,99718
Non-polymers4642
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, native gel electrophoresis, microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area77610 Å2
ΔGint-490 kcal/mol
Surface area143450 Å2

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Components

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Protein , 6 types, 10 molecules AEBFCGDHKN

#1: Protein Histone H3.2


Mass: 15251.830 Da / Num. of mol.: 2 / Mutation: K4(NLE), M90(NLE), M120(NLE), G102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pQE-81L / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G99R, A123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13498.715 Da / Num. of mol.: 2 / Mutation: K120C, S30T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P02281
#7: Protein Ubiquitin


Mass: 9036.393 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#10: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SET1 / Lysine N-methyltransferase 2 / SET domain-containing protein 1


Mass: 41508.488 Da / Num. of mol.: 1 / Fragment: UNP residues 762-1080
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SET1, KMT2, YTX1, YHR119W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi Five
References: UniProt: P38827, [histone H3]-lysine4 N-trimethyltransferase

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601 DNA (146- ... , 2 types, 2 molecules IJ

#5: DNA chain 601 DNA (146-MER)


Mass: 44825.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain 601 DNA (146-MER)


Mass: 45305.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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COMPASS component ... , 5 types, 6 molecules LMOPQR

#8: Protein COMPASS component SWD3 / Complex proteins associated with SET1 protein SWD3 / Set1C component SWD3


Mass: 34786.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWD3, CPS30, SAF35, YBR175W, YBR1237 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P38123
#9: Protein COMPASS component SWD1 / Complex proteins associated with SET1 protein SWD1 / Set1C component SWD1


Mass: 48702.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWD1, CPS50, SAF49, YAR003W, FUN16 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P39706
#11: Protein COMPASS component BRE2 / Brefeldin-A sensitivity protein 2 / Complex proteins associated with SET1 protein BRE2 / Set1C component BRE2


Mass: 58425.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRE2, CPS60, YLR015W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P43132
#12: Protein COMPASS component SDC1 / Complex proteins associated with SET1 protein SDC1 / Set1C component SDC1 / Suppressor of CDC25 protein 1


Mass: 19466.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SDC1, CPS25, SAF19, YDR469W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: Q03323
#13: Protein COMPASS component SPP1 / Complex proteins associated with SET1 protein SPP1 / Set1C component SPP1 / Suppressor of PRP protein 1


Mass: 45489.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPP1, CPS40, SAF41, YPL138C / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: Q03012

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Non-polymers , 2 types, 2 molecules

#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex between yeast COMPASS and a ubiquitinated NucleosomeCOMPLEX#1-#130MULTIPLE SOURCES
2Yeast COMPASSCOMPLEX#8-#131RECOMBINANT
3Ubiquitinated NucleosomeCOMPLEX#1-#71RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (brewer's yeast)4932
23Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
12Trichoplusia ni (cabbage looper)7111Hi FiveBacmid
23Escherichia coli (E. coli)562plasmid
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMTris1
2100 mMSodium ChlorideNaCl1
32 mMDTT1
425 uMS-adenosyl methionine1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 5 3.5 sec blot time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.96 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5784
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
4CTFFINDCTF correction
7UCSF Chimera1.13.1model fitting
8Coot0.8.9.1model fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2036654 / Details: Relion template-based picking from 3D model
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 650847 / Symmetry type: POINT
Atomic model buildingB value: 110 / Protocol: OTHER / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
16CHG

6chg

6CHG1
26BX3

6bx3

F6BX32
36BX3

6bx3

E6BX32799-850
46NJ9

6nj9

6NJ93

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