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- PDB-7oq4: Cryo-EM structure of the ATV RNAP Inhibitory Protein (RIP) bound ... -

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Basic information

Entry
Database: PDB / ID: 7oq4
TitleCryo-EM structure of the ATV RNAP Inhibitory Protein (RIP) bound to the DNA-binding channel of the host's RNA polymerase
Components
  • (DNA-directed RNA polymerase subunit ...) x 10
  • (DNA-directed RNA polymerase, subunit ...) x 2
  • Conserved protein
  • RNAP inhibitory protein
KeywordsVIRAL PROTEIN / viral inhibitor / transcription inhibition / ATV / archaeal virus / Archaea
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / 3 iron, 4 sulfur cluster binding / RNA polymerase III activity / RNA polymerase II activity / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / virion component / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...symbiont-mediated suppression of host transcription / 3 iron, 4 sulfur cluster binding / RNA polymerase III activity / RNA polymerase II activity / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / virion component / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
RIP/P131 family / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 ...RIP/P131 family / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / 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 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 / 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 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 ...FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 / RNAP inhibitory protein / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo4
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
Acidianus two-tailed virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsPilotto, S. / Fouqueau, T. / Lukoyanova, N. / Sheppard, C. / Lucas-Staat, S. / Diaz-Santin, L.M. / Matelska, D. / Prangishvili, D. / Cheung, A.C.M. / Werner, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust207446/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of RNA polymerase inhibition by viral and host factors.
Authors: Simona Pilotto / Thomas Fouqueau / Natalya Lukoyanova / Carol Sheppard / Soizick Lucas-Staat / Luis Miguel Díaz-Santín / Dorota Matelska / David Prangishvili / Alan C M Cheung / Finn Werner /
Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution ...RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
History
DepositionJun 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit A'
B: DNA-directed RNA polymerase subunit B
C: DNA-directed RNA polymerase subunit A''
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase subunit E
F: DNA-directed RNA polymerase, subunit F
G: DNA-directed RNA polymerase, subunit G
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
Q: Conserved protein
Z: RNAP inhibitory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,29622
Polymers422,58314
Non-polymers7138
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, single peak in superose 6 10/300 column, fluorescence resonance energy transfer, RIP binds inside the DNA-binding channel, mass spectrometry, all cross-linking contacts ...Evidence: gel filtration, single peak in superose 6 10/300 column, fluorescence resonance energy transfer, RIP binds inside the DNA-binding channel, mass spectrometry, all cross-linking contacts between RIP and RNAP support a 1:1 ratio
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area66950 Å2
ΔGint-452 kcal/mol
Surface area123860 Å2

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Components

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DNA-directed RNA polymerase subunit ... , 10 types, 10 molecules ABCDEHKLNP

#1: Protein DNA-directed RNA polymerase subunit A'


Mass: 99929.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P11512, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit B


Mass: 126647.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P11513, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit A'' / Subunit C


Mass: 44507.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P11514, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit D


Mass: 29858.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P39471, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit E


Mass: 20496.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P39466, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit H


Mass: 9477.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P11521, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit K


Mass: 10251.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P39463, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit L


Mass: 10061.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P46217, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase subunit N


Mass: 7673.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: P39472, DNA-directed RNA polymerase
#12: Protein/peptide DNA-directed RNA polymerase subunit P


Mass: 5662.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: Q4JAE8, DNA-directed RNA polymerase

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DNA-directed RNA polymerase, subunit ... , 2 types, 2 molecules FG

#6: Protein DNA-directed RNA polymerase, subunit F


Mass: 13070.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: Q4JB12, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase, subunit G


Mass: 15292.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rpoG, Saci_0661
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAY4, DNA-directed RNA polymerase

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Protein , 2 types, 2 molecules QZ

#13: Protein Conserved protein


Mass: 12331.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to add an additional copy of RPO8 labelled at the C-terminus with a hexa-his tag
References: UniProt: Q4JAJ6
#14: Protein RNAP inhibitory protein / RIP


Mass: 17321.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residual sequence from the thrombin cleavage site at the C-terminus of RIP (LVPR)
Source: (gene. exp.) Acidianus two-tailed virus / Plasmid: pET21a+
Details (production host): protein cloned within NdeI and XhoI restriction sites with a Thrombin cleavage site at the C-terminus of the protein sequence
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q3V4R7

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Non-polymers , 3 types, 8 molecules

#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4

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Details

Has ligand of interestN

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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: Complex of archaeal RNA-polymerase with the ATV inhibitory protein RIP
Type: COMPLEX
Details: The RNA polymerase was incubated with a 10-fold excess of RIP for 5 min at 338 K followed by cross-linking with BS3
Entity ID: #1-#14 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.421 MDa / Experimental value: YES
Buffer solutionpH: 7
Details: DTT was added fresh before the incubation of the two species
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidC8H18N2O4S1
2200 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
4100 microMzinc sulphateZnSO41
510 % w/vglycerolC3H8O31
65 mMdithiothreitolC4H10O2S21
SpecimenConc.: 0.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was monodisperse
Specimen supportDetails: after glow discharged, the grid was coated with graphene oxide
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 % / Chamber temperature: 277 K
Details: blotting force: -10 blotting time: 2 sec wait time: 0 sec

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: sample holder was tilted of -30 degrees for the entire data collection
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2130
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 45 / Used frames/image: 1-45

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION3particle selectionreference-based
2EPUimage acquisition
4GctfCTF correction
7PHENIX1.19model fittingDock in map
9cryoSPARC2initial Euler assignment2D classification
10cryoSPARC2final Euler assignment3D reconstruction
11cryoSPARC2classification3D reconstruction
12RELION33D reconstruction3D refinement, followed by three cycles of CTF refinement and post processing
13PHENIX1.19model refinementReal space refinement
Image processingDetails: The movie-stacks were aligned and summed using MotionCor2 within Relion 3.0
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 600640
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151237 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 81.4405 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient
Details: The C-terminal tail of RIP was manually built in Coot after the first refinement run.
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
17OH0

7oh0

1
23FAJ

3faj

A1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327149
ELECTRON MICROSCOPYf_angle_d0.5336670
ELECTRON MICROSCOPYf_dihedral_angle_d4.2583712
ELECTRON MICROSCOPYf_chiral_restr0.0444172
ELECTRON MICROSCOPYf_plane_restr0.0044706

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