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- PDB-7mei: Composite structure of EC+EC -

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Basic information

Entry
Database: PDB / ID: 7mei
TitleComposite structure of EC+EC
Components
  • (DNA (74-MER)) x 2
  • (DNA-directed RNA polymerase ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • (DNA-directed RNA polymerases II subunit ...) x 2
  • (Transcription initiation factor IIF subunit ...) x 2
  • RNA (5'-R(P*AP*AP*CP*UP*AP*GP*UP*UP*AP*AP*GP*AP*GP*GP*UP*U)-3')
  • RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*CP*CP*CP*AP*A)-3')
KeywordsTRANSCRIPTION / pol II
Function / homology
Function and homology information


: / : / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...: / : / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / : / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / RNA polymerase II general transcription initiation factor activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase III transcription / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / protein phosphatase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / positive regulation of translational initiation / Dual incision in TC-NER / : / : / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription-coupled nucleotide-excision repair / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / regulation of DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA polymerase; domain 1 - #390 / Gyrase A; domain 2 - #140 / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction ...DNA polymerase; domain 1 - #390 / Gyrase A; domain 2 - #140 / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / RNA polymerase Rpb1, domain 3 / Enzyme I; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RPB4 isoform 1 / RPC10 isoform 1 / TFG2 isoform 1 / RPB3 isoform 1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit ...DNA / DNA (> 10) / RNA / RNA (> 10) / RPB4 isoform 1 / RPC10 isoform 1 / TFG2 isoform 1 / RPB3 isoform 1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit beta / RPB11 isoform 1 / RPB10 isoform 1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / Transcription initiation factor IIF subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsYang, C. / Murakami, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2022
Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami /
Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / entity / entity_src_nat / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ref / struct_ref_seq
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 / _entity.pdbx_description / _entity_src_nat.common_name / _pdbx_entry_details.has_protein_modification / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

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Structure visualization

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Assembly

Deposited unit
N: DNA (74-MER)
O: DNA (74-MER)
a: DNA-directed RNA polymerase subunit
b: DNA-directed RNA polymerase subunit beta
c: DNA-directed RNA polymerase II subunit RPB3
d: DNA-directed RNA polymerase II subunit RPB4
e: DNA-directed RNA polymerases I, II, and III subunit RPABC1
f: DNA-directed RNA polymerases I, II, and III subunit RPABC2
g: DNA-directed RNA polymerase II subunit RPB7
h: DNA-directed RNA polymerases I, II, and III subunit RPABC3
i: DNA-directed RNA polymerase II subunit RPB9
j: DNA-directed RNA polymerases II subunit RPABC5
k: DNA-directed RNA polymerase II subunit RPB11
l: DNA-directed RNA polymerases II subunit RPABC4
r: RNA (5'-R(P*AP*AP*CP*UP*AP*GP*UP*UP*AP*AP*GP*AP*GP*GP*UP*U)-3')
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases II subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases II subunit RPABC4
R: RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*CP*CP*CP*AP*A)-3')
Q: Transcription initiation factor IIF subunit alpha
M: Transcription initiation factor IIF subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,213,88350
Polymers1,212,73930
Non-polymers1,14420
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules NO

#1: DNA chain DNA (74-MER)


Mass: 22801.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: DNA chain DNA (74-MER)


Mass: 22934.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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DNA-directed RNA polymerase ... , 7 types, 14 molecules aAbBcCdDgGiIkK

#3: Protein DNA-directed RNA polymerase subunit


Mass: 191821.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q1P2, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta


Mass: 138937.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q4H2, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 35330.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z3
#6: Protein DNA-directed RNA polymerase II subunit RPB4


Mass: 25451.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTI6
#9: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19081.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q270
#11: Protein DNA-directed RNA polymerase II subunit RPB9


Mass: 14308.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9EWC2
#13: Protein DNA-directed RNA polymerase II subunit RPB11


Mass: 13633.493 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7A1

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DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 6 molecules eEfFhH

#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1


Mass: 25117.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q456
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2


Mass: 17931.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16525.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8C2

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DNA-directed RNA polymerases II subunit ... , 2 types, 4 molecules jJlL

#12: Protein DNA-directed RNA polymerases II subunit RPABC5


Mass: 8290.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Q6
#14: Protein DNA-directed RNA polymerases II subunit RPABC4


Mass: 7729.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PY05

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RNA chain , 2 types, 2 molecules rR

#15: RNA chain RNA (5'-R(P*AP*AP*CP*UP*AP*GP*UP*UP*AP*AP*GP*AP*GP*GP*UP*U)-3')


Mass: 5003.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#16: RNA chain RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*CP*CP*CP*AP*A)-3')


Mass: 4677.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Transcription initiation factor IIF subunit ... , 2 types, 2 molecules QM

#17: Protein Transcription initiation factor IIF subunit alpha / TFIIF-alpha / TFIIF large subunit / Transcription factor G 105 kDa subunit / P105


Mass: 82320.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41895
#18: Protein Transcription initiation factor IIF subunit beta


Mass: 46684.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZ00

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Non-polymers , 2 types, 20 molecules

#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#20: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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

ComponentName: Head-to-end Colliding RNAPII Elongation / Type: COMPLEX
Details: bona fide transcription complex, which was generated from in vitro transcription system using isolated proteins from yeast, was achieved via glycerol gradient sedimentation
Entity ID: #1-#18 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.6 / Details: 20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4CTFFIND4.1.13CTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstructionpostprocessing
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2565746
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57690
Details: this is a composite structure composed of two parts. one part was finally calculated with 66261 parties to 3.54 angstrom , the other one part was finally calculated with 57690 particles to 3.54 angstrom .
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15C4J

5c4j

15C4J1PDBexperimental model
23PO2

3po2

13PO22PDBexperimental model
35FMF

5fmf

15FMF3PDBexperimental model

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