SAXSdb — 2gjk

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

Regulator of nonsense transcripts 1

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 295–914	Fragment：helicase core domain(residues 295-914)	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

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 2GJK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GK6 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 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 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 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 14 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

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	2gjk
Deposition date deposition_date	2006-03-31
Structure title title	Structural and functional insights into the human Upf1 helicase core
Keywords keywords	hupf1, helicase, NMD, HYDROLASE; HYDROLASE
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	26.23 Å
Radius of gyration Rg (electron density) rg_electron	25.31 Å
Forward intensity I(0) i0	78558600.00
Molecular weight molecular_weight	69397.0 kDa
Excluded volume excluded_volume	87083 Å³
Envelope volume envelope_volume	107280 Å³
Hydration-shell volume shell_volume	34276 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	33.57 Å
Envelope Rg envelope_rg	25.38 Å
Shape Rg shape_rg	25.34 Å
Total Rg total_rg	26.12 Å
Total atoms total_atoms	4876
Residues n_residues	614
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	78.1 Å
Rg (real space) rg_real	26.07 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	7.8560e+07
I(0) uncertainty (real space) i0_real_error	1.0730e+06
Rg (reciprocal space) rg_reciprocal	26.12 Å
I(0) (reciprocal space) i0_reciprocal	78560000.0000
Solution quality estimate total_estimate	0.8361
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.5 Å
Skewness Skewness skewness	0.138
Kurtosis Kurtosis kurtosis	-0.536
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16200000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Regulator of nonsense transcripts 1
Molecular weight formula_weight	70056.4 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4986

PLGSRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQFS

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2gjka1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d2gjka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d2gjka3
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.4 — Upf1 barrel domain-like
Family Family family	b.49.4.1 — Upf1 barrel domain-like

Domain ID domain_id	d2gjka4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2gjkA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gjkA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2gjkA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1240 —

Domain ID domain_id	2gjkA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	188.979 Å
Unit-cell length b length_b	188.979 Å
Unit-cell length c length_c	44.872 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2462
R_work r_work	0.2449
R_free r_free	0.2710

fit	/app/data/saxs_computation/gj/2gjk/2gjk.fit
pddf	/app/data/pr_computation/gj/2gjk/2gjk.pr.out
profile	/app/data/saxs_computation/gj/2gjk/2gjk.dat

Structural and functional insights into the human Upf1 helicase core

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

Regulator of nonsense transcripts 1

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