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3wbk

crystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex

Method: X-RAY DIFFRACTION Dmax: 121.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Eukaryotic translation initiation factor 5B

Saccharomyces cerevisiae

UniProt P39730

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 401–1002 Fragment：UNP residues 401-1002 Eukaryotic translation initiation factor 1A × 1 （P38912） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.30 Å R-free 0.317
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 401–1002 Fragment：UNP residues 401-1002 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.30 Å R-free 0.317

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 3WBK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3WBI Crystal structure analysis of eukaryotic translation initiation factor 5B structure I Deposited 2013-05-20 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 401–1002（602 aa） Fragment：UNP residues 401-1002
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.2M Tri-Sodium Citrate, 19% PEG 3350, HEPES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.268
3WBJ Crystal structure analysis of eukaryotic translation initiation factor 5B structure II Deposited 2013-05-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 401–855（455 aa） Fragment：UNP residues 401-855
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.1M Tris-HCl pH 8.0, 40% PEG 400, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.50 Å R-free 0.256
4N3S Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae, apo form Deposited 2013-10-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 399–852（454 aa） Fragment：unp residues 399-852
Not recorded GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；5 % PEG 3350 and 20 mM MgCl2., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.83 Å R-free 0.194
4N3S Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae, apo form Deposited 2013-10-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 399–852（454 aa） Fragment：unp residues 399-852
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；5 % PEG 3350 and 20 mM MgCl2., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.83 Å R-free 0.194
4NCF Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae in complex with GDP Deposited 2013-10-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 399–852（454 aa） Fragment：unp residues 399-852
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283 K；8 % PEG 8000 0.37 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 3.02 Å R-free 0.281
4NCF Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae in complex with GDP Deposited 2013-10-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 399–852（454 aa） Fragment：unp residues 399-852
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283 K；8 % PEG 8000 0.37 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 3.02 Å R-free 0.281
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain CP 401–739（339 aa） Fragment：DOMAIN 1 AND 2, RESIDUES 401-739
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain CV 401–739（339 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain 1 401–1000（600 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF2P_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–606； UniProt 401–1002 Author chain B； PDBConstruct 5–606； UniProt 401–1002

Eukaryotic translation initiation factor 1A

Saccharomyces cerevisiae

UniProt P38912

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 27–153 Fragment：UNP residues 27-153 Eukaryotic translation initiation factor 5B × 1 （P39730） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.30 Å R-free 0.317

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 3WBK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J80 CryoEM structure of 40S-eIF1-eIF1A preinitiation complex Deposited 2014-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 67 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT；pH 6.5；20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
cryo-EM vitrification conditions Blot for 2.5 seconds before plunging；120 K；Cryogen ETHANE；Blot for 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)
Resolution 3.75 Å
3J81 CryoEM structure of a partial yeast 48S preinitiation complex Deposited 2014-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 81 ZN ZINC ION × 3 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT；pH 6.5；20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
cryo-EM vitrification conditions Blot for 2.5 seconds before plunging；120 K；Cryogen ETHANE；Blot for 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)
Resolution 4.00 Å
3JAM CryoEM structure of 40S-eIF1A-eIF1 complex from yeast Deposited 2015-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 80 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT；pH 6.5；20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
cryo-EM vitrification conditions Blot for 2.5 to 3 seconds before plunging；120 K；Cryogen ETHANE；Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Resolution 3.46 Å
3JAP Structure of a partial yeast 48S preinitiation complex in closed conformation Deposited 2015-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 81 ZN ZINC ION × 4 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT；pH 6.5；20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
cryo-EM vitrification conditions Blot for 2.5 to 3 seconds before plunging；120 K；Cryogen ETHANE；Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Resolution 4.90 Å
6FYX Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1) Deposited 2018-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 117 ZN ZINC ION × 5 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6FYY Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2) Deposited 2018-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 117 ZN ZINC ION × 5 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
6GSM Structure of a partial yeast 48S preinitiation complex in open conformation. Deposited 2018-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 21–115（95 aa）
Not recorded 7NO [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate × 1 MG MAGNESIUM ION × 82 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6GSN Structure of a partial yeast 48S preinitiation complex in closed conformation Deposited 2018-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 5–115（111 aa）
Not recorded MG MAGNESIUM ION × 81 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.75 Å
6ZCE Structure of a yeast ABCE1-bound 43S pre-initiation complex Deposited 2020-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 45-meric
Chain i 1–153（153 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6ZU9 Structure of a yeast ABCE1-bound 48S initiation complex Deposited 2020-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain A 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8RW1 Structure of a yeast 48S-AUC preinitiation complex in closed conformation Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 115 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8S8D Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 116 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8S8E Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.1) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 116 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.85 Å
8S8F Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 116 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
8S8G Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.1) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 116 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8S8H Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.2) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 116 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8S8I Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF1) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 117 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8S8J Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 115 ZN ZINC ION × 4 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8S8K Structure of a yeast 48S-AUC preinitiation complex in swivelled conformation (model py48S-AUC-swiv-eIF1) Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain i 1–153（153 aa）
Not recorded MG MAGNESIUM ION × 96 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF1A_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 5–131； UniProt 27–153

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 3wbk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wbk
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3wbk
Deposition date deposition_date2013-05-20
Structure title titlecrystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex
Keywords keywordsflexible, eukaryotic translation initiation, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.57 Å
Radius of gyration Rg (electron density) rg_electron36.92 Å
Forward intensity I(0) i0257307000.00
Molecular weight molecular_weight132500.0 kDa
Excluded volume excluded_volume167610 ų
Envelope volume envelope_volume240170 ų
Hydration-shell volume shell_volume54564 ų
Envelope diameter envelope_diameter127.7 Å
Shell Rg shell_rg43.07 Å
Envelope Rg envelope_rg36.13 Å
Shape Rg shape_rg36.93 Å
Total Rg total_rg37.34 Å
Total atoms total_atoms9309
Residues n_residues1191
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 dmax121.2 Å
Rg (real space) rg_real37.43 Å
Rg uncertainty (real space) rg_real_error1.14 Å
I(0) (real space) i0_real2.5730e+08
I(0) uncertainty (real space) i0_real_error4.7170e+06
Rg (reciprocal space) rg_reciprocal37.52 Å
I(0) (reciprocal space) i0_reciprocal257300000.0000
Solution quality estimate total_estimate0.8866
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.1 Å
Skewness Skewness skewness0.221
Kurtosis Kurtosis kurtosis-0.363
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36080000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.882
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3wbkA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3wbkA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id3wbkA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10050 — Translation initiation factor IF- 2, domain 3
Domain ID domain_id3wbkA04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id3wbkB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3wbkB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id3wbkB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10050 — Translation initiation factor IF- 2, domain 3
Domain ID domain_id3wbkB04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
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8. Citations (1)

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9. Files and Curves (10)