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- PDB-5it9: Structure of the yeast Kluyveromyces lactis small ribosomal subun... -

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Entry
Database: PDB / ID: 5it9
TitleStructure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.
Components
  • (Ribosomal protein ...) x 33
  • 18S ribosomal RNA
  • Cricket paralysis virus IRES RNA
KeywordsRIBOSOME / IRES / small / subunit
Function / homology
Function and homology information


90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process ...90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S17 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 ...N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S17 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Diphtheria Toxin Repressor; domain 2 / N-terminal domain of TfIIb / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / SH3 type barrels. - #30 / K homology (KH) domain / Ribosomal protein L30/S12 / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Other non-globular / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / :
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / KLLA0F09812p / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12277p / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / 40S ribosomal protein S3 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / Small ribosomal subunit protein uS8 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / RPS23 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesCricket paralysis virus
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMurray, J. / Savva, C.G. / Shin, B.S. / Dever, T.E. / Ramakrishnan, V. / Fernandez, I.S.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
National Institutes of HealthIntramural Research Program United States
CitationJournal: Elife / Year: 2016
Title: Structural characterization of ribosome recruitment and translocation by type IV IRES.
Authors: Jason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández /
Abstract: Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps ...Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Derived calculations
Category: em_image_scans / em_software ...em_image_scans / em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name
Revision 1.2Dec 11, 2019Group: Advisory / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Assembly

Deposited unit
A: Ribosomal protein uS2
B: Ribosomal protein eS1
C: Ribosomal protein uS5
D: Ribosomal protein uS3
E: Ribosomal protein eS4
F: Ribosomal protein uS7
G: Ribosomal protein eS6
H: Ribosomal protein eS7
I: Ribosomal protein eS8
J: Ribosomal protein uS4
K: Ribosomal protein eS10
L: Ribosomal protein uS17
M: Ribosomal protein eS12
N: Ribosomal protein uS15
O: Ribosomal protein uS14
P: Ribosomal protein uS19
Q: Ribosomal protein uS9
R: Ribosomal protein eS17
S: Ribosomal protein uS13
T: Ribosomal protein eS19
U: Ribosomal protein uS10
V: Ribosomal protein eS21
W: Ribosomal protein uS8
X: Ribosomal protein uS21
Y: Ribosomal protein eS24
Z: Ribosomal protein eS25
a: Ribosomal protein eS26
b: Ribosomal protein eS27
c: Ribosomal protein eS28
d: Ribosomal protein eS29
e: Ribosomal protein eS30
f: Ribosomal protein eS31
g: Ribosomal protein RACK1
2: 18S ribosomal RNA
i: Cricket paralysis virus IRES RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,183,862118
Polymers1,181,72235
Non-polymers2,14183
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Ribosomal protein ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein Ribosomal protein uS2 / 40S ribosomal protein S0


Mass: 22882.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#2: Protein Ribosomal protein eS1 / 40S ribosomal protein S1


Mass: 24488.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#3: Protein Ribosomal protein uS5 / KLLA0F09812p


Mass: 23162.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#4: Protein Ribosomal protein uS3 / KLLA0D08305p


Mass: 24830.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#5: Protein Ribosomal protein eS4 / 40S ribosomal protein S4


Mass: 29486.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#6: Protein Ribosomal protein uS7 / KLLA0D10659p


Mass: 22912.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#7: Protein Ribosomal protein eS6 / 40S ribosomal protein S6


Mass: 25810.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#8: Protein Ribosomal protein eS7 / KLLA0C13519p


Mass: 21033.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#9: Protein Ribosomal protein eS8 / 40S ribosomal protein S8


Mass: 22511.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#10: Protein Ribosomal protein uS4 / KLLA0E23673p


Mass: 20882.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#11: Protein Ribosomal protein eS10 / KLLA0B08173p


Mass: 11423.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#12: Protein Ribosomal protein uS17 / KLLA0A10483p


Mass: 17712.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#13: Protein Ribosomal protein eS12 / 40S ribosomal protein S12


Mass: 13124.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#14: Protein Ribosomal protein uS15 / KLLA0F18040p


Mass: 16858.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#15: Protein Ribosomal protein uS14 / 40S ribosomal protein S14 / RP59


Mass: 13458.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#16: Protein Ribosomal protein uS19 / KLLA0F07843p


Mass: 14055.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#17: Protein Ribosomal protein uS9 / 40S ribosomal protein S16


Mass: 15656.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#18: Protein Ribosomal protein eS17 / KLLA0B01474p


Mass: 14728.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#19: Protein Ribosomal protein uS13 / KLLA0B01562p


Mass: 16953.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#20: Protein Ribosomal protein eS19 / KLLA0A07194p


Mass: 15747.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#21: Protein Ribosomal protein uS10 / KLLA0F25542p


Mass: 12032.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#22: Protein Ribosomal protein eS21 / 40S ribosomal protein S21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#23: Protein Ribosomal protein uS8 / 40S ribosomal protein S22


Mass: 14513.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#24: Protein Ribosomal protein uS21 / RPS23


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875M3
#25: Protein Ribosomal protein eS24 / 40S ribosomal protein S24


Mass: 15063.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#26: Protein Ribosomal protein eS25 / KLLA0B06182p


Mass: 7939.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#27: Protein Ribosomal protein eS26 / KLLA0D05115p


Mass: 11454.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#28: Protein Ribosomal protein eS27 / 40S ribosomal protein S27


Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#29: Protein Ribosomal protein eS28 / 40S ribosomal protein S28 / S33


Mass: 7073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#30: Protein Ribosomal protein eS29 / 40S ribosomal protein S29


Mass: 6322.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#31: Protein Ribosomal protein eS30 / KLLA0C04809p


Mass: 6329.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#32: Protein Ribosomal protein eS31 / Ubiquitin-40S ribosomal protein S27a


Mass: 7958.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#33: Protein Ribosomal protein RACK1 / KLLA0E12277p


Mass: 35612.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7

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RNA chain , 2 types, 2 molecules 2i

#34: RNA chain 18S ribosomal RNA


Mass: 573508.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#35: RNA chain Cricket paralysis virus IRES RNA


Mass: 61462.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricket paralysis virus / Production host: Escherichia coli (E. coli) / References: GenBank: 8895506

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Non-polymers , 2 types, 83 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Kluyveromyces lacti (yeast)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
120 milimolarMES-KOH1
2100 milimolarKCL1
38 milimolarMgCl(2)1
42 milimolarDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: OTHER
Electron lensMode: BRIGHT FIELD
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 / Classification: refinement
EM software
IDNameVersionCategory
1EPUparticle selection
2EPU1.8image acquisition
4CTFFINDCTF correction
9RELION1.4initial Euler assignment
13REFMAC5.8model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54481 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
RefinementResolution: 3.8→257.28 Å / Cor.coef. Fo:Fc: 0.848 / SU B: 43.619 / SU ML: 0.614 / σ(F): 0 / ESU R: 0.945
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rwork0.4131 --
obs0.4131 541724 100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso max: 500 Å2 / Biso mean: 119.994 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å26.48 Å2-4.09 Å2
2--5.72 Å2-0.25 Å2
3----5.06 Å2
Refinement stepCycle: final / Resolution: 3.8→257.28 Å
LigandSolventTotal
Num. atoms83 0 80144
Biso mean19.98 --
Num. residues--6820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01587007
X-RAY DIFFRACTIONr_bond_other_d0.0030.0258292
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.571125182
X-RAY DIFFRACTIONr_angle_other_deg1.2343136509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.7697.37312851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15922.5811701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34157302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5415405
X-RAY DIFFRACTIONr_chiral_restr0.3930.21214305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0266228
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0219071
X-RAY DIFFRACTIONr_mcbond_it2.75711.14619356
X-RAY DIFFRACTIONr_mcbond_other2.75811.14519355
X-RAY DIFFRACTIONr_mcangle_it5.27216.67224132
LS refinement shellResolution: 3.8→3.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.818 40236 -
obs--100 %

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