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7qg6

Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII

Method: X-RAY DIFFRACTION Dmax: 132.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Regulator of nonsense transcripts 3A

Homo sapiens

UniProt Q9H1J1

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: dimeric（2） Count mismatch; review required Chain A； UniProt 58–206 Chain C； UniProt 58–206 Chain E； UniProt 58–206 Chain G； UniProt 58–206 Not recorded Regulator of nonsense transcripts 2 × 4 （Q9HAU5） 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
2 Protein heterocomplex Heteromer Protein × 7 PDB declaration: dimeric（2） Count mismatch; review required Chain C； UniProt 58–206 Chain E； UniProt 58–206 Chain G； UniProt 58–206 Not recorded Regulator of nonsense transcripts 2 × 4 （Q9HAU5） 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
3 Protein heterocomplex Heteromer Protein × 7 PDB declaration: dimeric（2） Count mismatch; review required Chain C； UniProt 58–206 Chain E； UniProt 58–206 Chain G； UniProt 58–206 Not recorded Regulator of nonsense transcripts 2 × 4 （Q9HAU5） 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
4 Protein heterocomplex Heteromer Protein × 7 PDB declaration: dimeric（2） Count mismatch; review required Chain C； UniProt 58–206 Chain E； UniProt 58–206 Chain G； UniProt 58–206 Not recorded Regulator of nonsense transcripts 2 × 4 （Q9HAU5） 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

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 7QG6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2L08 Solution NMR Structure of Nonsense mRNA reducing factor 3A from H. Sapiens, Northeast Structural Genomics Consortium Target HR4714B Deposited 2010-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–155（86 aa） Fragment：sequence database residues 70-155
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100mM NaCl, 10mM Tris-HCl；Pressure ambient
NMR sample composition 0.82 mM [U-100% 13C; U-100% 15N] HR4714B, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-10% 13C; U-99% 15N] HR4714B, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name REN3A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 28–176； UniProt 58–206 Author chain C； PDBConstruct 28–176； UniProt 58–206 Author chain E； PDBConstruct 28–176； UniProt 58–206 Author chain G； PDBConstruct 28–176； UniProt 58–206

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 × 8 PDB declaration: dimeric（2） Count mismatch; review required Chain B； UniProt 761–1054 Chain D； UniProt 761–1054 Chain F； UniProt 761–1054 Chain H； UniProt 761–1054 Not recorded Regulator of nonsense transcripts 3A × 4 （Q9H1J1） 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
2 Protein heterocomplex Heteromer Protein × 7 PDB declaration: dimeric（2） Count mismatch; review required Chain B； UniProt 761–1054 Chain D； UniProt 761–1054 Chain F； UniProt 761–1054 Chain H； UniProt 761–1054 Not recorded Regulator of nonsense transcripts 3A × 3 （Q9H1J1） 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
3 Protein heterocomplex Heteromer Protein × 7 PDB declaration: dimeric（2） Count mismatch; review required Chain B； UniProt 761–1054 Chain D； UniProt 761–1054 Chain F； UniProt 761–1054 Chain H； UniProt 761–1054 Not recorded Regulator of nonsense transcripts 3A × 3 （Q9H1J1） 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
4 Protein heterocomplex Heteromer Protein × 7 PDB declaration: dimeric（2） Count mismatch; review required Chain B； UniProt 761–1054 Chain D； UniProt 761–1054 Chain F； UniProt 761–1054 Chain H； UniProt 761–1054 Not recorded Regulator of nonsense transcripts 3A × 3 （Q9H1J1） 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

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 7QG6 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
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

5 other PDB entries and 9 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 28–321； UniProt 761–1054 Author chain D； PDBConstruct 28–321； UniProt 761–1054 Author chain F； PDBConstruct 28–321； UniProt 761–1054 Author chain H； PDBConstruct 28–321； UniProt 761–1054

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 7qg6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7qg6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7qg6
Deposition date deposition_date2021-12-07
Structure title titleCo-crystal structure of UPF3A-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_guinier41.04 Å
Radius of gyration Rg (electron density) rg_electron40.54 Å
Forward intensity I(0) i0380757000.00
Molecular weight molecular_weight165770.0 kDa
Excluded volume excluded_volume210010 ų
Envelope volume envelope_volume291520 ų
Hydration-shell volume shell_volume60526 ų
Envelope diameter envelope_diameter143.7 Å
Shell Rg shell_rg45.66 Å
Envelope Rg envelope_rg39.73 Å
Shape Rg shape_rg40.52 Å
Total Rg total_rg40.90 Å
Total atoms total_atoms11716
Residues n_residues1458
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 dmax132.3 Å
Rg (real space) rg_real40.93 Å
Rg uncertainty (real space) rg_real_error1.14 Å
I(0) (real space) i0_real3.8080e+08
I(0) uncertainty (real space) i0_real_error7.2150e+06
Rg (reciprocal space) rg_reciprocal41.04 Å
I(0) (reciprocal space) i0_reciprocal380800000.0000
Solution quality estimate total_estimate0.6699
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.7 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.387
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48660000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 0.046; Positv: 1.000; Valcen: 0.992; Smooth: 0.851
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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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8. Citations (1)

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9. Files and Curves (10)