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2gk6

Structural and Functional insights into the human Upf1 helicase core

Method: X-RAY DIFFRACTION Dmax: 122.3 Å Quality: GOOD
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 295–914 Fragment：helicase core domain(residues 295-914) 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 295–914 Fragment：helicase core domain(residues 295-914) 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

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 2GK6 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 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
2GK7 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 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 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 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
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 A 115–914（800 aa） Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
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 B 115–914（800 aa） Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
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
2WJY Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form Deposited 2009-06-01 Different construct 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 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 5–624； UniProt 295–914 Author chain B； PDBConstruct 5–624； UniProt 295–914

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 2gk6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gk6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gk6
Deposition date deposition_date2006-03-31
Structure title titleStructural and Functional insights into the human Upf1 helicase core
Keywords keywordsUpf1, helicase, NMD, HYDROLASE; 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_guinier36.81 Å
Radius of gyration Rg (electron density) rg_electron36.52 Å
Forward intensity I(0) i0278617000.00
Molecular weight molecular_weight136100.0 kDa
Excluded volume excluded_volume171110 ų
Envelope volume envelope_volume231070 ų
Hydration-shell volume shell_volume52717 ų
Envelope diameter envelope_diameter129.2 Å
Shell Rg shell_rg42.85 Å
Envelope Rg envelope_rg36.13 Å
Shape Rg shape_rg36.51 Å
Total Rg total_rg36.97 Å
Total atoms total_atoms9562
Residues n_residues1204
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 dmax122.3 Å
Rg (real space) rg_real36.84 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real2.7860e+08
I(0) uncertainty (real space) i0_real_error4.3280e+06
Rg (reciprocal space) rg_reciprocal36.82 Å
I(0) (reciprocal space) i0_reciprocal278600000.0000
Solution quality estimate total_estimate0.8833
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.6 Å
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.362
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42050000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.902
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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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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2gk6a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd2gk6a2
Class classb — All beta proteins
Fold Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamilyb.49.4 — Upf1 barrel domain-like
Family Family familyb.49.4.1 — Upf1 barrel domain-like
Domain ID domain_idd2gk6a3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd2gk6a4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2gk6b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd2gk6b2
Class classb — All beta proteins
Fold Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamilyb.49.4 — Upf1 barrel domain-like
Family Family familyb.49.4.1 — Upf1 barrel domain-like
Domain ID domain_idd2gk6b3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.19 — Tandem AAA-ATPase domain
Domain ID domain_idd2gk6b4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id2gk6A01
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_id2gk6A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily230 —
Domain ID domain_id2gk6A03
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1240 —
Domain ID domain_id2gk6A04
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_id2gk6B01
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_id2gk6B02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily230 —
Domain ID domain_id2gk6B03
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1240 —
Domain ID domain_id2gk6B04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)