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- PDB-8q7z: Structure of the G. gallus 80S non-rotated ribosome -

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Basic information

Entry
Database: PDB / ID: 8q7z
TitleStructure of the G. gallus 80S non-rotated ribosome
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 16
  • (Large ribosomal subunit protein ...) x 13
  • (Ribosomal protein ...) x 17
  • (Small ribosomal subunit protein ...) x 11
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DNA-(apurinic or apyrimidinic site) lyase
  • Phe tRNA
  • Ubiquitin
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / translation
Function / homology
Function and homology information


TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / : / glucose 6-phosphate:phosphate antiporter activity / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha ...TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / : / glucose 6-phosphate:phosphate antiporter activity / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / RAD18 and ubiquitinated PCNA-mediated recruitment of translesion polymerases / Nucleotide Excision Repair / Deactivation of the beta-catenin transactivating complex / TRAF6 mediated induction of proinflammatory cytokines / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NFkB activation mediated by RIP1 complexed with activated TLR3 / Activated TAK1 mediates p38 MAP kinase phosphorylation / Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / MAPK6/MAPK4 signaling / Josephin domain DUBs / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / NFkB and MAPK activation mediated by TRAF6 upon TLR7 or TLR21 stimulation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / Neddylation
Similarity search - Function
Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Ribosomal protein L14, KOW motif / 40S ribosomal protein SA / Major facilitator superfamily / Major Facilitator Superfamily / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal ...Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Ribosomal protein L14, KOW motif / 40S ribosomal protein SA / Major facilitator superfamily / Major Facilitator Superfamily / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / MFS transporter superfamily / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL33 / Ribosomal protein L36a like / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L32 / Ribosomal protein S10 / Ribosomal protein L37 / 40S ribosomal protein S8 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL2 / 40S ribosomal protein S7 / DNA-(apurinic or apyrimidinic site) lyase / Ribosomal protein L15 / Ribosomal protein L26 like 1 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS13 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL13 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL30 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL28 / Ribosomal protein S14 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Ribosomal protein L19 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS9 / 60S ribosomal protein L21
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsNurullina, L. / Jenner, L. / Yusupov, M.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: FEBS Lett / Year: 2024
Title: Cryo-EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold-stress conditions.
Authors: Liliia Nurullina / Salvatore Terrosu / Alexander G Myasnikov / Lasse Bohl Jenner / Marat Yusupov /
Abstract: Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor ...Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor eEF2 with GDP, SERPINE1 mRNA binding protein 1 (SERBP1) and deacylated tRNA in the P/E position, showing common features with complexes already described in mammals. Modeling of most expansion segments of G. gallus 28S ribosomal RNA allowed us to identify specific features in their structural organization and to describe areas where a marked difference between mammalian and avian ribosomes could shed light on the evolution of the expansion segments. This study provides the first structure of an avian ribosome, establishing a model for future structural and functional studies on the translational machinery in Aves.
History
DepositionAug 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 2.0Mar 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entry_details / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B5: 28S rRNA
B8: 5.8S rRNA
B7: 5S rRNA
Az: 60S ribosomal protein L41
BA: 60S ribosomal protein L8
BB: Ribosomal protein uL3
BC: 60S ribosomal protein L4 C-terminal domain-containing protein
BD: Large ribosomal subunit protein uL18
BE: 60S ribosomal protein L6
BF: Large ribosomal subunit protein uL30
BG: Large ribosomal subunit protein eL8
BH: 60S ribosomal protein L9
BI: Large ribosomal subunit protein uL16
BJ: 60S ribosomal protein L11
BL: Large ribosomal subunit protein eL13
BM: 60S ribosomal protein L14
BN: Ribosomal protein L15
BO: Ribosomal protein uL13
BP: 60S ribosomal protein L17
BQ: Ribosomal protein L18
BR: Ribosomal protein L19
BS: 60S ribosomal protein L18a
BT: 60S ribosomal protein L21
BU: Large ribosomal subunit protein eL22
BV: Large ribosomal subunit protein uL14
BW: Ribosomal protein L24
BX: Ribosomal protein uL23
BY: Ribosomal protein L26 like 1
BZ: Large ribosomal subunit protein eL27
Ba: Ribosomal protein uL15
Bb: 60S ribosomal protein L29
Bc: Large ribosomal subunit protein eL30
Bd: 60S ribosomal protein L31
Be: Ribosomal protein L32
Bf: 60S ribosomal protein L35a
Bg: 60S ribosomal protein L34
Bh: Large ribosomal subunit protein uL29
Bi: Large ribosomal subunit protein eL36
Bj: Ribosomal protein L37
Bk: 60S ribosomal protein L38
Bl: Large ribosomal subunit protein eL39
Bm: Ubiquitin-60S ribosomal protein L40
Bo: Ribosomal protein L36a like
Bp: Large ribosomal subunit protein eL43
Br: 60S ribosomal protein L28
A2: 18S rRNA
Aa: Small ribosomal subunit protein eS1
AA: 40S ribosomal protein S27
AB: 40S ribosomal protein S28
Ab: 40S ribosomal protein S2
Ad: Small ribosomal subunit protein eS4
AD: Ribosomal protein eS30
AE: 40S ribosomal protein S26
Af: Small ribosomal subunit protein eS6
Ag: 40S ribosomal protein S7
Ah: 40S ribosomal protein S8
Ai: 40S ribosomal protein S9
Ak: 40S ribosomal protein S11
Am: Small ribosomal subunit protein uS15
An: Ribosomal protein S14
At: 40S ribosomal protein S20
Au: Small ribosomal subunit protein eS21
Av: 40S ribosomal protein S15a
Aw: Small ribosomal subunit protein uS12
Ax: 40S ribosomal protein S24
AZ: Small ribosomal subunit protein uS2
Ap: Ribosomal protein S16
AC: Ubiquitin
Ae: Ribosomal protein S5
AF: Small ribosomal subunit protein RACK1
AG: 40S ribosomal protein S29
Aj: Ribosomal protein S10
Al: Small ribosomal subunit protein eS12
Ao: Small ribosomal subunit protein uS19
Ar: 40S ribosomal protein S18
As: 40S ribosomal protein S19
Ay: 40S ribosomal protein S25
Ac: DNA-(apurinic or apyrimidinic site) lyase
V: Phe tRNA
Aq: Small ribosomal subunit protein eS17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,605,856581
Polymers3,593,39180
Non-polymers12,465501
Water106,3975906
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules B5B8B7A2V

#1: RNA chain 28S rRNA


Mass: 1439503.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#2: RNA chain 5.8S rRNA


Mass: 50446.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#3: RNA chain 5S rRNA


Mass: 38322.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: 63782
#46: RNA chain 18S rRNA


Mass: 588302.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#79: RNA chain Phe tRNA


Mass: 24593.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo

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60S ribosomal protein ... , 16 types, 16 molecules AzBABCBEBHBJBMBPBSBTBbBdBfBgBkBr

#4: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A087WNH4
#5: Protein 60S ribosomal protein L8


Mass: 28086.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NIX0
#7: Protein 60S ribosomal protein L4 C-terminal domain-containing protein


Mass: 46853.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZII1
#9: Protein 60S ribosomal protein L6


Mass: 34014.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q8UWG7
#12: Protein 60S ribosomal protein L9


Mass: 21871.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5NVI1
#14: Protein 60S ribosomal protein L11


Mass: 20269.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5P3B1
#16: Protein 60S ribosomal protein L14


Mass: 15514.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q98TF9
#19: Protein 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: A0A1D5PR40
#22: Protein 60S ribosomal protein L18a


Mass: 20856.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#23: Protein 60S ribosomal protein L21


Mass: 18622.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: R4GIQ2
#31: Protein 60S ribosomal protein L29


Mass: 8433.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1RNZ2
#33: Protein 60S ribosomal protein L31


Mass: 19836.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1RT94
#35: Protein 60S ribosomal protein L35a


Mass: 12609.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NQ35 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0YS49 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0YS49
#36: Protein 60S ribosomal protein L34


Mass: 13340.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1S0X5
#40: Protein 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1BU66
#45: Protein 60S ribosomal protein L28


Mass: 15920.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5F346

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Ribosomal protein ... , 17 types, 17 molecules BBBNBOBQBRBWBXBYBaBeBjBoADAnApAeAj

#6: Protein Ribosomal protein uL3


Mass: 46201.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZJZ2
#17: Protein Ribosomal protein L15


Mass: 24193.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NQG5
#18: Protein Ribosomal protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus sequence from PDB entry 7O7Z (XP_002723961.2 ) because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#20: Protein Ribosomal protein L18 / Ribosomal protein eL18


Mass: 21411.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#21: Protein Ribosomal protein L19


Mass: 23481.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZKK8
#26: Protein Ribosomal protein L24


Mass: 17837.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0XRE7
#27: Protein Ribosomal protein uL23


Mass: 17701.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the E1BS06 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V1AGP8 and two more sequences.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#28: Protein Ribosomal protein L26 like 1


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F2Z4K6
#30: Protein Ribosomal protein uL15


Mass: 16851.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NBX4 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZL98 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#34: Protein Ribosomal protein L32


Mass: 15955.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1BVB1
#39: Protein Ribosomal protein L37


Mass: 11103.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: E1C810
#43: Protein Ribosomal protein L36a like


Mass: 12335.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NIK4 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0YUB1 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0YUB1
#52: Protein Ribosomal protein eS30


Mass: 14536.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the A0A1D5PQV entry although it is an obsoleted entry, because no more entry in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#60: Protein Ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZHW8
#67: Protein Ribosomal protein S16


Mass: 16445.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: R4GGJ0
#69: Protein Ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: G1TFM5
#72: Protein Ribosomal protein S10


Mass: 18945.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1C4N0

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Large ribosomal subunit protein ... , 13 types, 13 molecules BDBFBGBIBLBUBVBZBcBhBiBlBp

#8: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34156.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P22451
#10: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 28844.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZJ56
#11: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


Mass: 30064.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P32429
#13: Protein Large ribosomal subunit protein uL16 / Ribosomal protein uL16 / 60S ribosomal protein L10 / Jun-binding protein JIF-1 / Ribosomal protein L10


Mass: 24506.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q08200
#15: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24455.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P41125
#24: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 14754.892 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF8
#25: Protein Large ribosomal subunit protein uL14 / Ribosomal protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZNU5 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#29: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P61355
#32: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12835.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P67883
#37: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF7
#38: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12331.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF6
#41: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6398.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q98TF5
#44: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10271.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P32046

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Protein , 3 types, 3 molecules BmACAc

#42: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14769.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: O42388
#68: Protein Ubiquitin


Mass: 18018.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P79781
#78: Protein DNA-(apurinic or apyrimidinic site) lyase


Mass: 26760.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
References: UniProt: F1NPA9, DNA-(apurinic or apyrimidinic site) lyase

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Small ribosomal subunit protein ... , 11 types, 11 molecules AaAdAfAmAuAwAZAFAlAoAq

#47: Protein Small ribosomal subunit protein eS1 / Ribosomal protein eS1


Mass: 29923.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#51: Protein Small ribosomal subunit protein eS4 / 40S ribosomal protein S4


Mass: 29652.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47836
#54: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6


Mass: 28723.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47838
#59: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q6ITC7
#62: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9157.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the E1BSJ2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZQ38 and A0A8V0ZC45 sequences.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#64: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23 / Ribosomal protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#66: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32945.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P50890
#70: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Receptor for activated C kinase ...Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated protein kinase C 1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P63247
#73: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 14569.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P84175
#74: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P62846
#80: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15566.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P08636

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40S ribosomal protein ... , 15 types, 15 molecules AAABAbAEAgAhAiAkAtAvAxAGArAsAy

#48: Protein 40S ribosomal protein S27


Mass: 9566.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q2TV39
#49: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q2U825
#50: Protein 40S ribosomal protein S2


Mass: 28875.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0Z891
#53: Protein 40S ribosomal protein S26


Mass: 13063.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZM66
#55: Protein 40S ribosomal protein S7


Mass: 22153.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NN16
#56: Protein 40S ribosomal protein S8


Mass: 24112.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NB02
#57: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: B7NZS8
#58: Protein 40S ribosomal protein S11


Mass: 18384.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TH5
#61: Protein 40S ribosomal protein S20


Mass: 13399.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NH93
#63: Protein 40S ribosomal protein S15a


Mass: 14881.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q3A7P6
#65: Protein 40S ribosomal protein S24


Mass: 15237.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NF89
#71: Protein 40S ribosomal protein S29


Mass: 18662.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0Z8V3
#75: Protein 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: G1TPG3
#76: Protein 40S ribosomal protein S19


Mass: 16118.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the A0A1D5PDV6 entry although it is an obsoleted entry, because no more sequence in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#77: Protein 40S ribosomal protein S25


Mass: 13746.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NU56 entry although it is an obsoleted entry, because no more sequence in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V1A7V4

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Non-polymers , 3 types, 6407 molecules

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


Mass: 24.305 Da / Num. of mol.: 494 / Source method: obtained synthetically / Formula: Mg
#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#83: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5906 / Source method: isolated from a natural source / Formula: H2O

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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: Gallus gallus 80S ribosome / Type: RIBOSOME / Details: Contains endogenous E-site tRNA / Entity ID: #1-#80 / Source: NATURAL
Molecular weightValue: 4.2 MDa / Experimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

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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: 96000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7PHENIXmodel fitting
9PHENIX1.19rc4_4035:model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 122598 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 7O7Z

7o7z


Accession code: 7O7Z / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006228844
ELECTRON MICROSCOPYf_angle_d0.652336440
ELECTRON MICROSCOPYf_dihedral_angle_d14.53682314
ELECTRON MICROSCOPYf_chiral_restr0.04241721
ELECTRON MICROSCOPYf_plane_restr0.00622039

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