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5a5t

Structure of mammalian eIF3 in the context of the 43S preinitiation complex

Method: ELECTRON MICROSCOPY Dmax: 186.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A

OrganismNot specified

UniProt G1SMZ5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–1362 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） UNCHARACTERIZED PROTEIN × 1 （G1SED9） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 1 1–1362（1362 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 1 1–1362（1362 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
8SUP Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES Deposited 2023-05-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain o 1–1362（1362 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9H74 Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA Deposited 2024-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain y 1–1362（1362 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail
cryo-EM vitrification conditions Cryogen ETHANE；The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
Resolution 2.90 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1SMZ5_RABIT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1362； UniProt 1–1362

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C

OrganismNot specified

UniProt G1U971

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 71–913 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） UNCHARACTERIZED PROTEIN × 1 （G1SED9） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 2 1–913（913 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 2 1–913（913 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
6YAM Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA Deposited 2020-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain v 1–913（913 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9CPA Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex Deposited 2024-07-18 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain k 1–913（913 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.00 Å
9H74 Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA Deposited 2024-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain v 1–913（913 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail
cryo-EM vitrification conditions Cryogen ETHANE；The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
Resolution 2.90 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1U971_RABIT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–843； UniProt 71–913

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E

OrganismNot specified

UniProt G1SUC8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 18–462 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） UNCHARACTERIZED PROTEIN × 1 （G1SED9） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 3 1–462（462 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 3 1–462（462 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
6YAM Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain w 18–462（445 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SUP Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES Deposited 2023-05-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain q 18–462（445 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CPA Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex Deposited 2024-07-18 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain Q 1–462（462 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.00 Å
9H74 Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA Deposited 2024-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain w 1–462（462 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail
cryo-EM vitrification conditions Cryogen ETHANE；The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
Resolution 2.90 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1SUC8_RABIT
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–445； UniProt 18–462

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F

OrganismNot specified

UniProt U3KNL5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain F； UniProt 1–364 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） UNCHARACTERIZED PROTEIN × 1 （G1SED9） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name U3KNL5_RABIT
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F； PDBConstruct 1–364； UniProt 1–364

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H

OrganismNot specified

UniProt G1ST95

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain H； UniProt 1–352 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） UNCHARACTERIZED PROTEIN × 1 （G1SED9） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 5 1–363（363 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 5 1–363（363 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
8SUP Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES Deposited 2023-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain s 12–363（352 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1ST95_RABIT
Isoform —
PDB entities 5
Chains and sequence ranges Author chain H； PDBConstruct 1–352； UniProt 1–352

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K

OrganismNot specified

UniProt G1T3L2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain K； UniProt 1–218 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） UNCHARACTERIZED PROTEIN × 1 （G1SED9） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 6 1–218（218 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 6 1–218（218 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
6YAM Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain s 1–218（218 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SUP Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES Deposited 2023-05-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain t 1–218（218 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CPA Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex Deposited 2024-07-18 Different oligomeric state Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain s 1–218（218 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.00 Å
9H74 Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA Deposited 2024-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain s 1–218（218 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail
cryo-EM vitrification conditions Cryogen ETHANE；The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
Resolution 2.90 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1T3L2_RABIT
Isoform —
PDB entities 6
Chains and sequence ranges Author chain K； PDBConstruct 1–218； UniProt 1–218

UNCHARACTERIZED PROTEIN

OrganismNot specified

UniProt G1SED9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain L； UniProt 43–606 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M × 1 （G1SLW8） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 7 1–607（607 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 7 1–607（607 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
8SUP Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES Deposited 2023-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain u 44–607（564 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CPA Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex Deposited 2024-07-18 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain t 44–607（564 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.00 Å
9H74 Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA Deposited 2024-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain t 1–607（607 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail
cryo-EM vitrification conditions Cryogen ETHANE；The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
Resolution 2.90 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1SED9_RABIT
Isoform —
PDB entities 7
Chains and sequence ranges Author chain L； PDBConstruct 1–564； UniProt 43–606

EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M

OrganismNot specified

UniProt G1SLW8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain M； UniProt 1–374 Not recorded EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A × 1 （G1SMZ5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C × 1 （G1U971） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E × 1 （G1SUC8） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F × 1 （U3KNL5） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H × 1 （G1ST95） EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K × 1 （G1T3L2） UNCHARACTERIZED PROTEIN × 1 （G1SED9） ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6W2S Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) Deposited 2020-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 43-meric
Chain 8 1–374（374 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.47 Å
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 8 1–374（374 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å
6YAM Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain u 1–374（374 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SUP Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES Deposited 2023-05-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain v 1–374（374 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CPA Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex Deposited 2024-07-18 Different oligomeric state Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain u 1–374（374 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.00 Å
9H74 Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA Deposited 2024-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain u 1–374（374 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM HEPES-KOH pH 7.4, 5 mM Mg(OAc)2, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT and Roche cOmplete protease inhibitor cocktail
cryo-EM vitrification conditions Cryogen ETHANE；The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
Resolution 2.90 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G1SLW8_RABIT
Isoform —
PDB entities 8
Chains and sequence ranges Author chain M； PDBConstruct 1–374； UniProt 1–374

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5a5t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5a5t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5a5t
Deposition date deposition_date2015-06-21
Structure title titleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Keywords keywordsHYDROLASE, EIF3, EUKARYOTIC INITIATION FACTOR 3, PREINITIATION COMPLEX, PCI/MPN CORE, EIF3G/I/B, EIF3D; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.95 Å
Radius of gyration Rg (electron density) rg_electron54.81 Å
Forward intensity I(0) i01854520000.00
Molecular weight molecular_weight361870.0 kDa
Excluded volume excluded_volume453880 ų
Envelope volume envelope_volume686260 ų
Hydration-shell volume shell_volume104140 ų
Envelope diameter envelope_diameter194.5 Å
Shell Rg shell_rg57.40 Å
Envelope Rg envelope_rg54.05 Å
Shape Rg shape_rg54.82 Å
Total Rg total_rg54.86 Å
Total atoms total_atoms25432
Residues n_residues3129
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax186.3 Å
Rg (real space) rg_real54.86 Å
Rg uncertainty (real space) rg_real_error1.70 Å
I(0) (real space) i0_real1.8550e+09
I(0) uncertainty (real space) i0_real_error3.5630e+07
Rg (reciprocal space) rg_reciprocal55.01 Å
I(0) (reciprocal space) i0_reciprocal1855000000.0000
Solution quality estimate total_estimate0.8797
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.2 Å
Skewness Skewness skewness0.266
Kurtosis Kurtosis kurtosis-0.377
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha128300000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.887
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)