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7nwu

Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII

Method: X-RAY DIFFRACTION Dmax: 125.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Regulator of nonsense transcripts 3B

Homo sapiens

UniProt Q9BZI7

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 49–170 Chain C； UniProt 49–170 Not recorded Regulator of nonsense transcripts 2 × 2 （Q9HAU5） 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；0.1M Ca acetate 0.1M MES 15% PEG 400 P 41 2 2 Resolution 2.60 Å R-free 0.256
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 49–170 Chain G； UniProt 49–170 Not recorded Regulator of nonsense transcripts 2 × 2 （Q9HAU5） 1PE PENTAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；0.1M Ca acetate 0.1M MES 15% PEG 400 P 41 2 2 Resolution 2.60 Å R-free 0.256

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 7NWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UW4 The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3 Deposited 2004-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 50–140（91 aa） Fragment：RRM DOMAIN, RESIDUES 50-140
Not recorded BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；100 MM AMMONIUM ACETATE, 15 MM MAGNESIUM ACETATE 50 MM SODIUM CACODYLATE 6.5, 8% ISOPROPANOL, pH 6.50
Resolution 1.95 Å R-free 0.227
1UW4 The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3 Deposited 2004-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 50–140（91 aa） Fragment：RRM DOMAIN, RESIDUES 50-140
Not recorded BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；100 MM AMMONIUM ACETATE, 15 MM MAGNESIUM ACETATE 50 MM SODIUM CACODYLATE 6.5, 8% ISOPROPANOL, pH 6.50
Resolution 1.95 Å R-free 0.227
2XB2 Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery Deposited 2010-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain U 411–470（60 aa） Fragment：C-TERMINAL EJC BINDING REGION, RESIDUES 411-470
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M NA-CACODYLATE PH 6.5, 0.2M MG-ACETATE 4H2O, 10 % PEG 8000
Resolution 3.40 Å R-free 0.260
2XB2 Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery Deposited 2010-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain G 411–470（60 aa） Fragment：C-TERMINAL EJC BINDING REGION, RESIDUES 411-470
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M NA-CACODYLATE PH 6.5, 0.2M MG-ACETATE 4H2O, 10 % PEG 8000
Resolution 3.40 Å R-free 0.260

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

View Construct and Data Evidence
UniProt name REN3B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–122； UniProt 49–170 Author chain C； PDBConstruct 1–122； UniProt 49–170 Author chain E； PDBConstruct 1–122； UniProt 49–170 Author chain G； PDBConstruct 1–122； UniProt 49–170

Regulator of nonsense transcripts 2

Homo sapiens

UniProt Q9HAU5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 767–1017 Chain D； UniProt 767–1017 Not recorded Regulator of nonsense transcripts 3B × 2 （Q9BZI7） 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；0.1M Ca acetate 0.1M MES 15% PEG 400 P 41 2 2 Resolution 2.60 Å R-free 0.256
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain F； UniProt 767–1017 Chain H； UniProt 767–1017 Not recorded Regulator of nonsense transcripts 3B × 2 （Q9BZI7） 1PE PENTAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；0.1M Ca acetate 0.1M MES 15% PEG 400 P 41 2 2 Resolution 2.60 Å R-free 0.256

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 7NWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UW4 The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3 Deposited 2004-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 768–1015（248 aa） Fragment：MIF4G DOMAIN, RESIDUES 768-1015
Not recorded BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；100 MM AMMONIUM ACETATE, 15 MM MAGNESIUM ACETATE 50 MM SODIUM CACODYLATE 6.5, 8% ISOPROPANOL, pH 6.50
Resolution 1.95 Å R-free 0.227
1UW4 The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3 Deposited 2004-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 768–1015（248 aa） Fragment：MIF4G DOMAIN, RESIDUES 768-1015
Not recorded BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；100 MM AMMONIUM ACETATE, 15 MM MAGNESIUM ACETATE 50 MM SODIUM CACODYLATE 6.5, 8% ISOPROPANOL, pH 6.50
Resolution 1.95 Å R-free 0.227
2WJV Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Deposited 2009-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1105–1198（94 aa） Fragment：C-TERMINAL REGION, RESIDUES 1105-1198
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.5-1.6M AMMONIUM SULPHATE, 100 MM MES PH 6.3-6.5 AND 2% V/V GLYCEROL
Resolution 2.85 Å R-free 0.248
2WJV Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Deposited 2009-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1105–1198（94 aa） Fragment：C-TERMINAL REGION, RESIDUES 1105-1198
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.5-1.6M AMMONIUM SULPHATE, 100 MM MES PH 6.3-6.5 AND 2% V/V GLYCEROL
Resolution 2.85 Å R-free 0.248
4CEK Crystal structure of the second MIF4G domain of human nonsense mediated decay factor UPF2 Deposited 2013-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 455–757（303 aa） Fragment：MIF4G2, RESIDUES 455-757
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；100 MM MES PH 6.0, 19% PEG 3350 AND AT A PROTEIN CONCENTRATION OF 8 MG/ML
Resolution 2.35 Å R-free 0.251
4CEM Crystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2 Deposited 2013-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 121–486（366 aa） Fragment：MIF4G1, RESIDUES 121-486
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；100 MM BICINE PH 9, 100 MM NACL, 11% PEG 6000 AND AT A PROTEIN CONCENTRATION OF 16 MG/ML
Resolution 2.60 Å R-free 0.251
4CEM Crystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2 Deposited 2013-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 121–486（366 aa） Fragment：MIF4G1, RESIDUES 121-486
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；100 MM BICINE PH 9, 100 MM NACL, 11% PEG 6000 AND AT A PROTEIN CONCENTRATION OF 16 MG/ML
Resolution 2.60 Å R-free 0.251
7QG6 Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: dimeric
Chain B 761–1054（294 aa）
Chain D 761–1054（294 aa）
Chain F 761–1054（294 aa）
Chain H 761–1054（294 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M Sodium HEPES pH 7.0 10% w/v PEG 4000 10% v/v 2-Propanol
Resolution 2.95 Å R-free 0.263
7QG6 Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: dimeric
Chain B 761–1054（294 aa）
Chain D 761–1054（294 aa）
Chain F 761–1054（294 aa）
Chain H 761–1054（294 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M Sodium HEPES pH 7.0 10% w/v PEG 4000 10% v/v 2-Propanol
Resolution 2.95 Å R-free 0.263
7QG6 Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: dimeric
Chain B 761–1054（294 aa）
Chain D 761–1054（294 aa）
Chain F 761–1054（294 aa）
Chain H 761–1054（294 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M Sodium HEPES pH 7.0 10% w/v PEG 4000 10% v/v 2-Propanol
Resolution 2.95 Å R-free 0.263
7QG6 Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: dimeric
Chain B 761–1054（294 aa）
Chain D 761–1054（294 aa）
Chain F 761–1054（294 aa）
Chain H 761–1054（294 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M Sodium HEPES pH 7.0 10% w/v PEG 4000 10% v/v 2-Propanol
Resolution 2.95 Å R-free 0.263

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RENT2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–251； UniProt 767–1017 Author chain D； PDBConstruct 1–251； UniProt 767–1017 Author chain F； PDBConstruct 1–251； UniProt 767–1017 Author chain H； PDBConstruct 1–251； UniProt 767–1017

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 7nwu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7nwu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7nwu
Deposition date deposition_date2021-03-17
Structure title titleCo-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII
Keywords keywordsnonsense mediated mRNA decay neurological development x-linked intellectual disability up-frameshift proteins, RNA BINDING PROTEIN; RNA BINDING 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_guinier40.23 Å
Radius of gyration Rg (electron density) rg_electron39.62 Å
Forward intensity I(0) i0412726000.00
Molecular weight molecular_weight171180.0 kDa
Excluded volume excluded_volume216430 ų
Envelope volume envelope_volume291350 ų
Hydration-shell volume shell_volume61373 ų
Envelope diameter envelope_diameter134.1 Å
Shell Rg shell_rg45.21 Å
Envelope Rg envelope_rg39.01 Å
Shape Rg shape_rg39.59 Å
Total Rg total_rg40.07 Å
Total atoms total_atoms12088
Residues n_residues1466
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 dmax125.7 Å
Rg (real space) rg_real40.10 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real4.1270e+08
I(0) uncertainty (real space) i0_real_error6.9090e+06
Rg (reciprocal space) rg_reciprocal40.23 Å
I(0) (reciprocal space) i0_reciprocal412800000.0000
Solution quality estimate total_estimate0.8886
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.8 Å
Skewness Skewness skewness0.165
Kurtosis Kurtosis kurtosis-0.455
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha58990000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.732
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7nwuA01
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)