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- PDB-6nmi: Cryo-EM structure of the human TFIIH core complex -

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Entry
Database: PDB / ID: 6nmi
TitleCryo-EM structure of the human TFIIH core complex
Components
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription factor IIH subunit ...) x 5
  • CDK-activating kinase assembly factor MAT1
KeywordsTRANSCRIPTION / DNA repair / helicase / multiprotein complex
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / ventricular system development / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / central nervous system myelin formation / regulation of mitotic recombination / erythrocyte maturation ...cyclin-dependent protein kinase activating kinase holoenzyme complex / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / ventricular system development / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / central nervous system myelin formation / regulation of mitotic recombination / erythrocyte maturation / nucleotide-excision repair factor 3 complex / hair follicle maturation / adult heart development / hair cell differentiation / transcription factor TFIIH core complex / embryonic cleavage / transcription factor TFIIH holo complex / negative regulation of DNA helicase activity / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / UV protection / transcription initiation from RNA polymerase I promoter / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / transcription elongation from RNA polymerase I promoter / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase I transcription / 3'-5' DNA helicase activity / ATPase activator activity / transcription factor TFIID complex / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / bone mineralization / spinal cord development / hematopoietic stem cell differentiation / transcription by RNA polymerase I / 7-methylguanosine mRNA capping / DNA topological change / transcriptional preinitiation complex / regulation of cyclin-dependent protein serine/threonine kinase activity / DNA-dependent ATPase activity / embryonic organ development / regulation of mitotic cell cycle phase transition / transcription elongation from RNA polymerase II promoter / response to UV / DNA helicase / helicase activity / DNA helicase activity / nucleotide-excision repair, DNA duplex unwinding / promoter-specific chromatin binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / chromosome segregation / nucleotide-excision repair / nucleotide-excision repair, DNA incision, 5'-to lesion / protein localization / positive regulation of DNA binding / nucleotide-excision repair, DNA incision / protein-macromolecule adaptor activity / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / positive regulation of smooth muscle cell proliferation / transcription-coupled nucleotide-excision repair / spindle / response to calcium ion / multicellular organism growth / 4 iron, 4 sulfur cluster binding / cell population proliferation / protein-containing complex assembly / double-stranded DNA binding / transcription by RNA polymerase II / extracellular matrix organization / G2/M transition of mitotic cell cycle / protein N-terminus binding / transcription initiation from RNA polymerase II promoter / response to oxidative stress / in utero embryonic development / nucleic acid binding / protein C-terminus binding / response to hypoxia / damaged DNA binding / aging / ATPase activity / nuclear speck / positive regulation of apoptotic process / regulation of transcription by RNA polymerase II / DNA repair / apoptotic process / transcription factor binding / nucleolus / chromatin binding / protein phosphorylation / viral process / negative regulation of apoptotic process / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding
Helicase conserved C-terminal domain / Ssl1-like / ATP-dependent helicase Rad3/Chl1-like / TFIIH subunit Ssl1/p44 / PH-like domain superfamily / Helical and beta-bridge domain / DEAD2 / TFIIH subunit TTDA/Tfb5 / Helicase/UvrB, N-terminal / ATP-dependent helicase, C-terminal ...Helicase conserved C-terminal domain / Ssl1-like / ATP-dependent helicase Rad3/Chl1-like / TFIIH subunit Ssl1/p44 / PH-like domain superfamily / Helical and beta-bridge domain / DEAD2 / TFIIH subunit TTDA/Tfb5 / Helicase/UvrB, N-terminal / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / BSD domain / TFIIH subunit Tfb4/GTF2H3 / Transcription factor TFIIH subunit p52/Tfb2 / TFIIH C1-like domain / Zinc finger C2H2-type / Cdk-activating kinase assembly factor MAT1/Tfb3 / Transcription factor Tfb2 (p52) C-terminal domain / Ubiquitin interacting motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / von Willebrand factor, type A / RAD3/XPD family / Type III restriction enzyme, res subunit / Zinc finger, RING-type / Helicase, C-terminal / Transcription factor Tfb2 / Helicase XPB/Ssl2 / TFIIH p62 subunit, N-terminal domain / BSD domain / Zinc finger, RING/FYVE/PHD-type / Ssl1-like / TFIIH p62 subunit, N-terminal / Transcription factor TFIIH complex subunit Tfb5 / DEAD_2 / Helical and beta-bridge domain / Helicase C-terminal domain / Transcription factor Tfb2, C-terminal domain / von Willebrand factor A-like domain superfamily / Helicase XPB/Ssl2, N-terminal domain / ERCC3/RAD25/XPB helicase, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / TFIIH subunit Tfb1/GTF2H1 / Zinc finger, RING-type, conserved site / Cdk-activating kinase assembly factor MAT1, centre / Zinc finger, C3HC4 type (RING finger) / CDK-activating kinase assembly factor MAT1 / TFB5-like superfamily / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / TFIIH C1-like domain / Helicase superfamily 1/2, ATP-binding domain / Transcription factor Tfb4 / TFB5-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 1 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4 / General transcription factor IIH subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 3
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGreber, B.J. / Toso, D. / Fang, J. / Nogales, E.
Funding support United States, Switzerland, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM063210 United States
Swiss National Science FoundationP300PA_160983 Switzerland
Swiss National Science FoundationP300PA_174355 Switzerland
CitationJournal: Elife / Year: 2019
Title: The complete structure of the human TFIIH core complex.
Authors: Basil J Greber / Daniel B Toso / Jie Fang / Eva Nogales /
Abstract: Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is ...Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: General transcription and DNA repair factor IIH helicase subunit XPB
B: General transcription and DNA repair factor IIH helicase subunit XPD
C: General transcription factor IIH subunit 1, p62
D: General transcription factor IIH subunit 4, p52
E: General transcription factor IIH subunit 2, p44
F: General transcription factor IIH subunit 3, p34
G: General transcription factor IIH subunit 5, p8
H: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,38915
Polymers388,6458
Non-polymers7447
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules AB

#1: Protein General transcription and DNA repair factor IIH helicase subunit XPB


Mass: 74233.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P19447*PLUS, DNA helicase
#2: Protein General transcription and DNA repair factor IIH helicase subunit XPD


Mass: 86417.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P18074*PLUS

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General transcription factor IIH subunit ... , 5 types, 5 molecules CDEFG

#3: Protein General transcription factor IIH subunit 1, p62


Mass: 57789.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P32780*PLUS
#4: Protein General transcription factor IIH subunit 4, p52 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q92759
#5: Protein General transcription factor IIH subunit 2, p44


Mass: 39609.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q13888*PLUS
#6: Protein General transcription factor IIH subunit 3, p34 / p34 / BASIC TRANSCRIPTION FACTOR 2 34 KDA SUBUNIT / BTF2 P34 / GENERAL TRANSCRIPTION FACTOR IIH ...p34 / BASIC TRANSCRIPTION FACTOR 2 34 KDA SUBUNIT / BTF2 P34 / GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 3 / TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P34 SUBUNIT


Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q13889
#7: Protein General transcription factor IIH subunit 5, p8 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q6ZYL4

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Protein , 1 types, 1 molecules H

#8: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 35873.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P51948

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Non-polymers , 2 types, 7 molecules

#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsThe full sequence for General transcription factor IIH subunit 1, p62 ...The full sequence for General transcription factor IIH subunit 1, p62 MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGK AKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQE DPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDG CNGLRYNLTSDIIESIFRTYPAVKMKYAENVPHNMTEKEFWTRFFQSHYFHRDRLNTGSK DLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPSASNSKSIKENSN AAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPSNMDGNSGDADCFQPAVKRAKLQESIEY EDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIRQEMEAYTPKLTQ VLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFP VNTPFLEEKVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQ SRRLMKKT General transcription and DNA repair factor IIH helicase subunit XPB MGKRDRADRDKKKSRKRHYEDEEDDEEDAPGNDPQEAVPSAAGKQVDESGTKVDEYGAKD YRLQMPLKDDHTSRPLWVAPDGHIFLEAFSPVYKYAQDFLVAIAEPVCRPTHVHEYKLTA YSLYAAVSVGLQTSDITEYLRKLSKTGVPDGIMQFIKLCTVSYGKVKLVLKHNRYFVESC HPDVIQHLLQDPVIRECRLRNSEGEATELITETFTSKSAISKTAESSGGPSTSRVTDPQG KSDIPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRND SVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKR CLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRS WEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDL NFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNK FRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNP KINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFY SLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLAAT DLDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRSKAPSKHVHPLFKRF RK General transcription factor IIH subunit 1 MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGK AKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQE DPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDG CNGLRYNLTSDIIESIFRTYPAVKMKYAENVPHNMTEKEFWTRFFQSHYFHRDRLNTGSK DLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPSASNSKSIKENSN AAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPSNMDGNSGDADCFQPAVKRAKLQESIEY EDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIRQEMEAYTPKLTQ VLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFP VNTPFLEEKVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQ SRRLMKKT General transcription and DNA repair factor IIH helicase subunit XPD MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQ RAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPE VTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDL KALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNID NVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARE TDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSG LAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEP FDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMAT FTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFT SYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVA RGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHA AQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYF LRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQL

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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: Transcription factor IIH (TFIIH) / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8 / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
Buffer component
IDConc.NameBuffer-ID
120 mMHepes-KOH1
2150 mMSodium chloride1
35 mMMagnesium chloride1
40.015 %NP40 substitute1
51.5 %Glycerol1
62 %Trehalose1
SpecimenConc.: 0.0049 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gatan Solarus / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Residual beam tilt corrected in RELION 3.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 43478 X / Nominal defocus max: 700 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8.25 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 7 / Num. of real images: 21437
Details: Images were collected as dose-fractionated movie frames (33 or 50 frames per exposure).
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Phase plate: A Thermo Fisher Scientific Volta Phase Plate was used.

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Processing

SoftwareName: PHENIX / Version: 1.14_3211: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4GctfCTF correctionCTF determination
5RELION3CTF correctionCTF correction
8UCSF Chimeramodel fittingInitial fitting
9Cootmodel fittingRebuilding
10Omodel fittingRebuilding
12RELION3initial Euler assignment
13RELION3final Euler assignment
14RELION3classification
15RELION33D reconstruction
16PHENIXmodel refinementReal Space Refine
CTF correctionDetails: CTF correction during 3D reconstruction in RELION 3.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138659 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Reference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced de novo.
Atomic model building
IDPDB-ID3D fitting-ID
15OF41
24ERN1
35OQJ1
41G251
55O851
62DII1
72JNJ1

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