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4cem

Crystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2

Method: X-RAY DIFFRACTION Dmax: 137.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 121–486 Fragment：MIF4G1, RESIDUES 121-486 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 121–486 Fragment：MIF4G1, RESIDUES 121-486 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 4CEM 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 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
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 RENT2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–370； UniProt 121–486 Author chain B； PDBConstruct 5–370； UniProt 121–486

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 4cem

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4cem
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4cem
Deposition date deposition_date2013-11-11
Structure title titleCrystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2
Keywords keywordsTRANSCRIPTION; TRANSCRIPTION
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_guinier34.07 Å
Radius of gyration Rg (electron density) rg_electron33.83 Å
Forward intensity I(0) i085526100.00
Molecular weight molecular_weight72083.0 kDa
Excluded volume excluded_volume89749 ų
Envelope volume envelope_volume122960 ų
Hydration-shell volume shell_volume32876 ų
Envelope diameter envelope_diameter149.3 Å
Shell Rg shell_rg36.63 Å
Envelope Rg envelope_rg34.99 Å
Shape Rg shape_rg33.79 Å
Total Rg total_rg34.21 Å
Total atoms total_atoms5061
Residues n_residues611
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 dmax137.6 Å
Rg (real space) rg_real34.55 Å
Rg uncertainty (real space) rg_real_error2.03 Å
I(0) (real space) i0_real8.5530e+07
I(0) uncertainty (real space) i0_real_error1.6660e+06
Rg (reciprocal space) rg_reciprocal34.25 Å
I(0) (reciprocal space) i0_reciprocal85500000.0000
Solution quality estimate total_estimate0.7338
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.9 Å
Skewness Skewness skewness0.792
Kurtosis Kurtosis kurtosis0.492
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12800000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.396; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.490; Smooth: 0.858
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4cemA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily180 —
Domain ID domain_id4cemB00
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)