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2wjv

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2

Method: X-RAY DIFFRACTION Dmax: 202.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

REGULATOR OF NONSENSE TRANSCRIPTS 1

HOMO SAPIENS

UniProt Q92900

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 115–914 Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914 REGULATOR OF NONSENSE TRANSCRIPTS 2 × 1 （Q9HAU5） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 115–914 Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914 REGULATOR OF NONSENSE TRANSCRIPTS 2 × 1 （Q9HAU5） 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

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 2WJV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GJK Structural and functional insights into the human Upf1 helicase core Deposited 2006-03-31 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 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；295 K；50mM MES, 0.5-3% PEG4000, 0.005mM MgSO4, 10mM DTT, pH 6.0, EVAPORATION, temperature 295K
Resolution 2.60 Å R-free 0.271
2GK6 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 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 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；295 K；100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, EVAPORATION, temperature 295K
Resolution 2.40 Å R-free 0.272
2GK6 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 Different construct 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 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；295 K；100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, EVAPORATION, temperature 295K
Resolution 2.40 Å R-free 0.272
2GK7 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 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 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.8；295 K；100mM Na/K Phosphate, 6-8% PEG3350, 10mM DTT, pH 5.8, EVAPORATION, temperature 295K
Resolution 2.80 Å R-free 0.298
2IYK Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1 Deposited 2006-07-18 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 115–272（158 aa） Fragment：UPF2-INTERACTING DOMAIN, RESIDUES 115-272
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；30% PENTAERYTHRITOL ETHOXYLATE (15/4EO/OH) (V/V), 50 MM AMMONIUM SULPHATE,50 MM BIS-TRIS PH 6.5
Resolution 2.95 Å R-free 0.259
2IYK Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1 Deposited 2006-07-18 Different construct 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 115–272（158 aa） Fragment：UPF2-INTERACTING DOMAIN, RESIDUES 115-272
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；30% PENTAERYTHRITOL ETHOXYLATE (15/4EO/OH) (V/V), 50 MM AMMONIUM SULPHATE,50 MM BIS-TRIS PH 6.5
Resolution 2.95 Å R-free 0.259
2WJY Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form Deposited 2009-06-01 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 115–914（800 aa） Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.6M AMMONIUM SULPHATE, 100 MM MES PH 6, 10% DIOXANE
Resolution 2.50 Å R-free 0.240
2XZO Upf1 helicase - RNA complex Deposited 2010-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 295–914（620 aa） Fragment：HELICASE DOMAIN, RESIDUES 295-914
Not recorded 1PE PENTAETHYLENE GLYCOL × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；100 MM SODIUM ACETATE PH 4.6, 20 MM CACL2, 15% MPD
Resolution 2.40 Å R-free 0.233
2XZP Upf1 helicase Deposited 2010-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 295–914（620 aa） Fragment：HELICASE DOMAIN, RESIDUES 295-914
Not recorded GOL GLYCEROL × 9 MLI MALONATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；50MM SODIUM CITRATE PH 6.0, 1.5M SODIUM MALONATE
Resolution 2.72 Å R-free 0.214
6EJ5 A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner Deposited 2017-09-20 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 295–925（631 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；291 K；1.4 M sodium malonate, 50 mM sodium citrate pH 6.2
Resolution 3.34 Å R-free 0.309
6Z3R Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ Deposited 2020-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1085–1095（11 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.97 Å
8RXB Human UPF1 CH domain in complex with SMG6 peptide Deposited 2024-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 115–287（173 aa）
Chain D 115–287（173 aa）
Chain E 115–287（173 aa）
Chain I 115–287（173 aa）
Chain L 115–287（173 aa）
Chain P 115–287（173 aa）
Not recorded ZN ZINC ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；solution (28% (w/v) PEG 3500, 0.2M Lithium sulfate and 0.1 M Tris pH 7.8)
Resolution 2.60 Å R-free 0.295
9QWN Human UPF1 in complex with the histone stem loop RNA Deposited 2025-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 115–914（800 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

11 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RENT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–800； UniProt 115–914 Author chain B； PDBConstruct 1–800； UniProt 115–914

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 D； UniProt 1105–1198 Fragment：C-TERMINAL REGION, RESIDUES 1105-1198 REGULATOR OF NONSENSE TRANSCRIPTS 1 × 1 （Q92900） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1105–1198 Fragment：C-TERMINAL REGION, RESIDUES 1105-1198 REGULATOR OF NONSENSE TRANSCRIPTS 1 × 1 （Q92900） 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

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 2WJV 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 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 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
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 RENT2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 4–97； UniProt 1105–1198 Author chain E； PDBConstruct 4–97； UniProt 1105–1198

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 2wjv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2wjv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2wjv
Deposition date deposition_date2009-06-01
Structure title titleCrystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2
Keywords keywordsHYDROLASE, ZINC-FINGER, ATP-BINDING, RNA-BINDING, NONSENSE-MEDIATED MRNA DECAY, NUCLEOTIDE-BINDING, METAL-BINDING; HYDROLASE
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_guinier52.80 Å
Radius of gyration Rg (electron density) rg_electron53.65 Å
Forward intensity I(0) i0538344000.00
Molecular weight molecular_weight188700.0 kDa
Excluded volume excluded_volume235260 ų
Envelope volume envelope_volume349340 ų
Hydration-shell volume shell_volume60815 ų
Envelope diameter envelope_diameter221.9 Å
Shell Rg shell_rg49.28 Å
Envelope Rg envelope_rg53.35 Å
Shape Rg shape_rg53.57 Å
Total Rg total_rg53.77 Å
Total atoms total_atoms13187
Residues n_residues1654
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 dmax202.8 Å
Rg (real space) rg_real53.62 Å
Rg uncertainty (real space) rg_real_error3.58 Å
I(0) (real space) i0_real5.3830e+08
I(0) uncertainty (real space) i0_real_error1.2560e+07
Rg (reciprocal space) rg_reciprocal52.14 Å
I(0) (reciprocal space) i0_reciprocal537300000.0000
Solution quality estimate total_estimate0.5074
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary54.1 Å
Skewness Skewness skewness0.807
Kurtosis Kurtosis kurtosis0.390
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23600000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.428; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.742; Smooth: 0.546
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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) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id2wjvA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2wjvA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily230 —
Domain ID domain_id2wjvA04
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1240 —
Domain ID domain_id2wjvA05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2wjvB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2wjvB03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily230 —
Domain ID domain_id2wjvB04
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1240 —
Domain ID domain_id2wjvB05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2wjvD01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily770 —
Domain ID domain_id2wjvD02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily160 —
Domain ID domain_id2wjvE01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily770 —
Domain ID domain_id2wjvE02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily160 —
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8. Citations (1)

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9. Files and Curves (10)