SAXSdb — 4cek

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1. Protein Identity and Related Structures Protein Identity & Related Structures

REGULATOR OF NONSENSE TRANSCRIPTS 2

HOMO SAPIENS

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 455–757	Fragment：MIF4G2, RESIDUES 455-757	No other associated polymer	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

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 4CEK	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 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 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 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 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
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 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 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 12 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 5–307； UniProt 455–757

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4cek
Deposition date deposition_date	2013-11-11
Structure title title	Crystal structure of the second MIF4G domain of human nonsense mediated decay factor UPF2
Keywords keywords	TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.10 Å
Radius of gyration Rg (electron density) rg_electron	19.07 Å
Forward intensity I(0) i0	13942000.00
Molecular weight molecular_weight	28001.0 kDa
Excluded volume excluded_volume	35138 Å³
Envelope volume envelope_volume	41707 Å³
Hydration-shell volume shell_volume	18582 Å³
Envelope diameter envelope_diameter	72.5 Å
Shell Rg shell_rg	25.15 Å
Envelope Rg envelope_rg	19.44 Å
Shape Rg shape_rg	19.05 Å
Total Rg total_rg	20.03 Å
Total atoms total_atoms	1958
Residues n_residues	240
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	73.2 Å
Rg (real space) rg_real	20.09 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	1.3940e+07
I(0) uncertainty (real space) i0_real_error	2.1000e+05
Rg (reciprocal space) rg_reciprocal	20.10 Å
I(0) (reciprocal space) i0_reciprocal	13940000.0000
Solution quality estimate total_estimate	0.8409
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.390
Kurtosis Kurtosis kurtosis	-0.123
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3672000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.659; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.998

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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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8. Citations (1)

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Unit-cell length a length_a	40.880 Å
Unit-cell length b length_b	56.600 Å
Unit-cell length c length_c	142.220 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	71.070 Å
R factor r_factor	0.2085
R_work r_work	0.2062
R_free r_free	0.2508

Description description	REGULATOR OF NONSENSE TRANSCRIPTS 2
Molecular weight formula_weight	35610.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1990

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

REGULATOR OF NONSENSE TRANSCRIPTS 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

fit	/app/data/saxs_computation/ce/4cek/4cek.fit
pddf	/app/data/pr_computation/ce/4cek/4cek.pr.out
profile	/app/data/saxs_computation/ce/4cek/4cek.dat