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1uw4

The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3

Method: X-RAY DIFFRACTION Dmax: 107.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UPF3X

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 50–140 Fragment：RRM DOMAIN, RESIDUES 50-140 REGULATOR OF NONSENSE TRANSCRIPTS 2 × 1 （Q9HAU5） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 50–140 Fragment：RRM DOMAIN, RESIDUES 50-140 REGULATOR OF NONSENSE TRANSCRIPTS 2 × 1 （Q9HAU5） 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

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 1UW4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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
7NWU Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 49–170（122 aa）
Chain C 49–170（122 aa）
Not recorded 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
7NWU Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 49–170（122 aa）
Chain G 49–170（122 aa）
Not recorded 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

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

View Construct and Data Evidence
UniProt name Q9BZI7
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–91； UniProt 50–140 Author chain C； PDBConstruct 1–91； UniProt 50–140

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 768–1015 Fragment：MIF4G DOMAIN, RESIDUES 768-1015 UPF3X × 1 （Q9BZI7） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 768–1015 Fragment：MIF4G DOMAIN, RESIDUES 768-1015 UPF3X × 1 （Q9BZI7） 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

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 1UW4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2WJV Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Deposited 2009-06-01 Different construct 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 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 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
7NWU Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 767–1017（251 aa）
Chain D 767–1017（251 aa）
Not recorded 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
7NWU Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII Deposited 2021-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 767–1017（251 aa）
Chain H 767–1017（251 aa）
Not recorded 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
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 Q9HAU5
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–248； UniProt 768–1015 Author chain D； PDBConstruct 1–248； UniProt 768–1015

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 1uw4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1uw4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1uw4
Deposition date deposition_date2004-01-29
Structure title titleThe structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3
Keywords keywordsNONSENSE MEDIATED MRNA DECAY PROTEIN, RNA-BINDING PROTEIN, NMD, RNP DOMAIN, MIF4G DOMAIN, 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_guinier31.49 Å
Radius of gyration Rg (electron density) rg_electron31.11 Å
Forward intensity I(0) i095077100.00
Molecular weight molecular_weight80209.0 kDa
Excluded volume excluded_volume101690 ų
Envelope volume envelope_volume130540 ų
Hydration-shell volume shell_volume36276 ų
Envelope diameter envelope_diameter112.2 Å
Shell Rg shell_rg36.81 Å
Envelope Rg envelope_rg30.89 Å
Shape Rg shape_rg31.07 Å
Total Rg total_rg31.79 Å
Total atoms total_atoms5659
Residues n_residues678
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 dmax107.0 Å
Rg (real space) rg_real31.63 Å
Rg uncertainty (real space) rg_real_error1.08 Å
I(0) (real space) i0_real9.5080e+07
I(0) uncertainty (real space) i0_real_error1.4720e+06
Rg (reciprocal space) rg_reciprocal31.58 Å
I(0) (reciprocal space) i0_reciprocal95070000.0000
Solution quality estimate total_estimate0.8587
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.2 Å
Skewness Skewness skewness0.479
Kurtosis Kurtosis kurtosis-0.236
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25430000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.789
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1uw4a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family familyd.58.7.4 — Smg-4/UPF3
Domain ID domain_idd1uw4b_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.14 — MIF4G domain-like
Domain ID domain_idd1uw4c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family familyd.58.7.4 — Smg-4/UPF3
Domain ID domain_idd1uw4d_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.14 — MIF4G domain-like

CATH v4.4 (4 domains)

Domain ID domain_id1uw4A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id1uw4B00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily180 —
Domain ID domain_id1uw4C00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id1uw4D00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily180 —
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8. Citations (1)

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9. Files and Curves (10)