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- PDB-9fpz: Human NatA-MAP2 80S ribosome complex -

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Basic information

Entry
Database: PDB / ID: 9fpz
TitleHuman NatA-MAP2 80S ribosome complex
Components
  • (60S ribosomal protein ...) x 6
  • (Large ribosomal subunit protein ...) x 2
  • (N-alpha-acetyltransferase ...) x 2
  • 28S rRNA
  • 5.8S rRNA (58-MER)
  • Methionine aminopeptidase 2
KeywordsTRANSLATION / co-translational processing / ribosome associated factor (RAF) / methionine aminopeptidase 2 (MAP2) / N-terminal methionine excision (NME) / N-acetyl-transferase A (NatA) / N-termional acetylation (NTA) / UBA domain / a-solenoid / protein-protein and protein-RNA interactions
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / methionyl aminopeptidase ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / N-acetyltransferase activity / acetyltransferase activator activity / metalloexopeptidase activity / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / axial mesoderm development / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / regulation of translational initiation / middle ear morphogenesis / protein acetylation / metalloaminopeptidase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / chromosome organization / aminopeptidase activity / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / cytosolic ribosome / ossification / positive regulation of translation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / skeletal system development / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / cellular response to gamma radiation / protein processing / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / cellular response to UV / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / ribosome binding / cell body / angiogenesis / transcription regulator complex / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / postsynaptic density / rRNA binding / protein stabilization / nuclear body / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / focal adhesion / intracellular membrane-bounded organelle / mRNA binding / synapse / dendrite / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / endoplasmic reticulum / DNA binding / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Acetyltransferase (GNAT) family / Ribosomal protein L28e / Tetratricopeptide repeat / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L6e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / TPR repeat region circular profile. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal Protein L6, KOW domain / 60S ribosomal protein L35 / Ribosomal protein L6e / 60S ribosomal protein L19 / 60S ribosomal protein L6E / TPR repeat profile. / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Acyl-CoA N-acyltransferase / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Tetratricopeptide repeats / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Tetratricopeptide repeat / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 ...: / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Methionine aminopeptidase 2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL6 / N-alpha-acetyltransferase 15, NatA auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsKlein, M.A. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome.
Authors: Marius Klein / Klemens Wild / Irmgard Sinning /
Abstract: Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine ...Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common combination of subsequent modifications carried out on the 80S ribosome. How these enzymatic processes are coordinated in the context of a rapidly translating ribosome has remained elusive. Here, we report two cryo-EM structures of multi-enzyme complexes assembled on vacant human 80S ribosomes, indicating two routes for NME-NTA. Both assemblies form on the 80S independent of nascent chain substrates. Irrespective of the route, NatA occupies a non-intrusive 'distal' binding site on the ribosome which does not interfere with MAP1 or MAP2 binding nor with most other ribosome-associated factors (RAFs). NatA can partake in a coordinated, dynamic assembly with MAP1 through the hydra-like chaperoning function of the abundant Nascent Polypeptide-Associated Complex (NAC). In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Together, our data provide the structural framework for the coordinated orchestration of NME and NTA in protein biogenesis.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / em_admin / entity / entity_poly / entity_poly_seq / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq
Item: _atom_site.label_seq_id / _citation.country ..._atom_site.label_seq_id / _citation.country / _citation.journal_abbrev / _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.name / _em_admin.last_update / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _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 / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: N-alpha-acetyltransferase 10
8: 5.8S rRNA (58-MER)
A: Methionine aminopeptidase 2
B: N-alpha-acetyltransferase 15, NatA auxiliary subunit
1: 28S rRNA
LC: 60S ribosomal protein L4
LE: Large ribosomal subunit protein eL6
Lk: 60S ribosomal protein L38
LY: Large ribosomal subunit protein uL24
Lh: 60S ribosomal protein L35
LX: 60S ribosomal protein L23a
LR: 60S ribosomal protein L19
Lr: 60S ribosomal protein L28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,009,27316
Polymers2,008,49513
Non-polymers7783
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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N-alpha-acetyltransferase ... , 2 types, 2 molecules 2B

#1: Protein N-alpha-acetyltransferase 10 / N-terminal acetyltransferase complex ARD1 subunit homolog A / hARD1 / NatA catalytic subunit Naa10


Mass: 20003.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA10, ARD1, ARD1A, TE2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA
#4: Protein N-alpha-acetyltransferase 15, NatA auxiliary subunit / Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / ...Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / Protein tubedown-1 / Tbdn100


Mass: 98658.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15, GA19, NARG1, NATH, TBDN100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXJ9

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RNA chain , 2 types, 2 molecules 81

#2: RNA chain 5.8S rRNA (58-MER)


Mass: 18646.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#5: RNA chain 28S rRNA


Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 1 types, 1 molecules A

#3: Protein Methionine aminopeptidase 2 / MAP 2 / MetAP 2 / Initiation factor 2-associated 67 kDa glycoprotein / p67 / p67eIF2 / Peptidase M


Mass: 53413.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase

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60S ribosomal protein ... , 6 types, 6 molecules LCLkLhLXLRLr

#6: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#8: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#10: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#11: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#12: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#13: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779

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Large ribosomal subunit protein ... , 2 types, 2 molecules LELY

#7: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#9: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17174.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254

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Non-polymers , 2 types, 3 molecules

#14: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#15: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

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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: human NatA and MAP2 bound to the PTE of the 80S ribosome
Type: RIBOSOME / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 41.28 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25404 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330687
ELECTRON MICROSCOPYf_angle_d0.71943044
ELECTRON MICROSCOPYf_dihedral_angle_d20.7458408
ELECTRON MICROSCOPYf_chiral_restr0.0385027
ELECTRON MICROSCOPYf_plane_restr0.0044140

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