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2nlw

Solution structure of the RRM domain of human eukaryotic initiation factor 3b

Method: SOLUTION NMR Dmax: 60.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Eukaryotic translation initiation factor 3 subunit 9

Homo sapiens

UniProt P55884

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 170–274 Fragment：RNA Recognition Motif No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.5；298 K；Ionic strength (raw mmCIF value) 300mM；Pressure ambient NMR sample composition：0.8mM eIF3b-RRM unlabeled, 20mM HEPES, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.8mM eIF3b-RRM U-15N, 20mM HEPES, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.8mM eIF3b-RRM U-15N,13C, 20mM HEPES, 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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 2NLW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KRB Solution structure of EIF3B-RRM bound to EIF3J peptide Deposited 2009-12-16 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 184–264（81 aa） Fragment：RRM domain, UNP residues 184-264
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure AMBIENT
NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] eIF3b-RRM, 0.85 mM eIF3j peptide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM eIF3b-RRM, 0.85 mM [U-100% 13C; U-100% 15N] eIF3j peptide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] eIF3b-RRM, 0.85 mM eIF3j peptide, 100% D2O | 100% D2O
Resolution not provided
5K1H eIF3b relocated to the intersubunit face to interact with eIF1 and below the eIF2 ternary-complex. from the structure of a partial yeast 48S preinitiation complex in closed conformation. Deposited 2016-05-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 170–745（576 aa） Fragment：UNP Residues 170-745
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
6YBT Structure of a human 48S translational initiation complex - eIF3bgi Deposited 2020-03-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain 1 1–814（814 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
6ZMW Structure of a human 48S translational initiation complex Deposited 2020-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain 1 1–814（814 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 89 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZON SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1 Deposited 2020-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 48-meric
Chain B 1–814（814 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZP4 SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 Deposited 2020-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain B 1–814（814 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZVJ Structure of a human ABCE1-bound 43S pre-initiation complex - State II Deposited 2020-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 51-meric
Chain B 180–745（566 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7A09 Structure of a human ABCE1-bound 43S pre-initiation complex - State III Deposited 2020-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain B 1–814（814 aa）
Not recorded ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7QP6 Structure of the human 48S initiation complex in open state (h48S AUG open) Deposited 2022-01-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric
Chain 1 1–813（813 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.
Resolution 4.70 Å
7QP7 Structure of the human 48S initiation complex in closed state (h48S AUG closed) Deposited 2022-01-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–813（813 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.
Resolution 3.70 Å
8OZ0 Structure of a human 48S translation initiation complex with eIF4F and eIF4A Deposited 2023-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain I 1–814（814 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 89 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8PJ1 Structure of human 48S translation initiation complex in open codon scanning state (48S-1) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain 1 1–814（814 aa）
Not recorded MG MAGNESIUM ION × 90 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.40 Å
8PJ2 Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain 1 1–814（814 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.40 Å
8PJ3 Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain 1 1–814（814 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.70 Å
8PJ4 Structure of human 48S translation initiation complex after eIF5 release (48S-4) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric
Chain 1 1–814（814 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.20 Å
8PJ5 Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–814（814 aa）
Not recorded MG MAGNESIUM ION × 91 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.90 Å
8PJ6 Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain 1 1–814（814 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.90 Å
8XXN Cryo-EM structure of the human 43S ribosome with PDCD4 Deposited 2024-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 50-meric
Chain 3B 1–814（814 aa）
Not recorded MG MAGNESIUM ION × 23 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF39_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–105； UniProt 170–274

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 2nlw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2nlw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2nlw
Deposition date deposition_date2006-10-20
Structure title titleSolution structure of the RRM domain of human eukaryotic initiation factor 3b
Keywords keywordstranslation initiation, eukaryotic initiation factor 3 complex, RNA recognition motif, TRANSLATION; TRANSLATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.40 Å
Radius of gyration Rg (electron density) rg_electron15.00 Å
Forward intensity I(0) i0491338000.00
Molecular weight molecular_weight190950.0 kDa
Excluded volume excluded_volume240480 ų
Envelope volume envelope_volume44029 ų
Hydration-shell volume shell_volume19159 ų
Envelope diameter envelope_diameter64.0 Å
Shell Rg shell_rg25.67 Å
Envelope Rg envelope_rg20.19 Å
Shape Rg shape_rg14.92 Å
Total Rg total_rg15.60 Å
Total atoms total_atoms26784
Residues n_residues1680
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 dmax60.6 Å
Rg (real space) rg_real15.46 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real4.9130e+08
I(0) uncertainty (real space) i0_real_error6.2060e+06
Rg (reciprocal space) rg_reciprocal15.45 Å
I(0) (reciprocal space) i0_reciprocal491300000.0000
Solution quality estimate total_estimate0.7695
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.6 Å
Skewness Skewness skewness0.516
Kurtosis Kurtosis kurtosis0.244
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha288600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.431; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.707; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2nlwA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
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8. Citations (1)

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9. Files and Curves (10)