SAXSdb — 6jwi

▼

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

Ubiqutin

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 8 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 1–76 Chain I； UniProt 1–76	Non-standard monomer：Yes (specific site not provided by mmCIF)	Nuclear protein localization protein 4 × 1 （P33755） alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 8 ZN ZINC ION × 2 BCN BICINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate	Resolution 2.55 Å R-free 0.226

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A5JUZ1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–76； UniProt 1–76 Author chain I； PDBConstruct 1–76； UniProt 1–76

Nuclear protein localization protein 4

Saccharomyces cerevisiae S288c

UniProt P33755

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 8 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 113–580	Not recorded	Ubiqutin × 2 （A5JUZ1） alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 8 ZN ZINC ION × 2 BCN BICINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate	Resolution 2.55 Å R-free 0.226
2	Other combination Monomer Protein × 1 其他Polymer 6 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 113–580	Not recorded	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 6 ZN ZINC ION × 2 BCN BICINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate	Resolution 2.55 Å R-free 0.226

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 6JWI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6JWH Yeast Npl4 zinc finger, MPN and CTD domains Deposited 2019-04-20	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 113–580（468 aa）	Mutation：E123A,K124A,E125A	ZN ZINC ION × 2 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；4% Tacsimat (pH 6.0), 12% PEG 3350	Resolution 1.72 Å R-free 0.193
6JWJ Npl4 in complex with Ufd1 Deposited 2019-04-20	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 A 113–580（468 aa）	Mutation：E123A,K124A,E125A	ZN ZINC ION × 2 GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；90mM BisTris-HCl (pH 7.5), 19% PEG 3350, 10mM ATP	Resolution 1.58 Å R-free 0.206
6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.	Resolution 3.90 Å
6OAA Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1 Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–580（580 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.	Resolution 4.10 Å
8DAR Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP Deposited 2022-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.00 Å
8DAS Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA) Deposited 2022-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.50 Å
8DAT Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB) Deposited 2022-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.80 Å
8DAU Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) Deposited 2022-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.70 Å
8DAV Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uC) Deposited 2022-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.50 Å
8DAW Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) Deposited 2022-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.60 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric	Chain G 1–580（580 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å

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

View Construct and Data Evidence

UniProt name	NPL4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 6–473； UniProt 113–580 Author chain E； PDBConstruct 6–473； UniProt 113–580

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6jwi
Deposition date deposition_date	2019-04-20
Structure title title	Yeast Npl4 in complex with Lys48-linked diubiquitin
Keywords keywords	UBIQUITIN, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	37.37 Å
Radius of gyration Rg (electron density) rg_electron	36.71 Å
Forward intensity I(0) i0	255771000.00
Molecular weight molecular_weight	127710.0 kDa
Excluded volume excluded_volume	159080 Å³
Envelope volume envelope_volume	216250 Å³
Hydration-shell volume shell_volume	49424 Å³
Envelope diameter envelope_diameter	134.2 Å
Shell Rg shell_rg	42.19 Å
Envelope Rg envelope_rg	37.20 Å
Shape Rg shape_rg	36.62 Å
Total Rg total_rg	37.35 Å
Total atoms total_atoms	8946
Residues n_residues	1059
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

▼

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

Maximum dimension Dmax dmax	126.7 Å
Rg (real space) rg_real	37.36 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	2.5580e+08
I(0) uncertainty (real space) i0_real_error	3.9750e+06
Rg (reciprocal space) rg_reciprocal	37.37 Å
I(0) (reciprocal space) i0_reciprocal	255800000.0000
Solution quality estimate total_estimate	0.8891
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.2 Å
Skewness Skewness skewness	0.307
Kurtosis Kurtosis kurtosis	-0.371
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51510000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.956

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ubiqutin
Molecular weight formula_weight	8623.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,G
Atom count atom_count	9116

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear protein localization protein 4
Molecular weight formula_weight	53939.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E

GPLGSIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 branched

Description description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	BICINE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6jwig_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6jwii_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

▶

8. Citations (1)

▶

Unit-cell length a length_a	86.351 Å
Unit-cell length b length_b	103.103 Å
Unit-cell length c length_c	99.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	48.990 Å
R factor r_factor	0.1924
R_work r_work	0.1905
R_free r_free	0.2257

fit	/app/data/saxs_computation/jw/6jwi/6jwi.fit
pddf	/app/data/pr_computation/jw/6jwi/6jwi.pr.out
profile	/app/data/saxs_computation/jw/6jwi/6jwi.dat

Yeast Npl4 in complex with Lys48-linked diubiquitin

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

Ubiqutin

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear protein localization protein 4

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)