SAXSdb — 3vht

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

Green fluorescent protein,ATPase WRNIP1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 9–46	Fragment：GFP,Wrnip1 UBZ domain (UNP RESIDUES 9-46) Non-standard monomer：Yes (specific site not provided by mmCIF)	Green fluorescent protein × 1 Ubiquitin × 1 （P62983） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M DL-Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.238

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 3VHT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3VHS Crystal structure of UBZ of human WRNIP1 Deposited 2011-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 17–40（24 aa） Fragment：UBIQUITIN-BINDING ZINC FINGER DOMAIN (UNP RESIDUES 17-40) Chain B 17–40（24 aa） Fragment：UBIQUITIN-BINDING ZINC FINGER DOMAIN (UNP RESIDUES 17-40)	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；28% PEG 400, 0.1M HEPES, 0.2M calcium chrolide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.262

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	WRIP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 234–271； UniProt 9–46

Ubiquitin

OrganismNot specified

UniProt P62983

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–76	Not recorded	Green fluorescent protein × 1 Green fluorescent protein,ATPase WRNIP1 × 1 （Q96S55） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M DL-Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.238

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 3VHT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GVI Zebrafish USP30 in complex with Lys6-linked diubiquitin Deposited 2016-09-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Chain C 1–72（72 aa）	Mutation：K6R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；90 mM Tris-HCl, 180 mM ammonium acetate, 23% PEG3350, 10 mM TCEP	Resolution 1.87 Å R-free 0.206
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Chain C 1–76（76 aa）	Mutation：K63R	XYZ beta-D-xylofuranose × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2	Resolution 1.78 Å R-free 0.245
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Mutation：K63R	XYZ beta-D-xylofuranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2	Resolution 1.78 Å R-free 0.245
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Chain D 1–76（76 aa）	Mutation：K63R	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate	Resolution 2.25 Å R-free 0.239
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–76（76 aa） Chain H 1–76（76 aa）	Mutation：K63R	GOL GLYCEROL × 1 PR PRASEODYMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate	Resolution 2.25 Å R-free 0.239
5XIU Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin Deposited 2017-04-27	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 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG3350, 0.1 M Tris-HCl (pH8.5), 0.2 M Ammonium Acetate	Resolution 1.80 Å R-free 0.207
7E62 Mouse TAB2 NZF in complex with Lys6-linked diubiquitin Deposited 2021-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–77（77 aa）	Mutation：K6R Mutation：A77D	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM HEPES-NaOH (pH 7.5), 1.44 M sodium citrate	Resolution 1.99 Å R-free 0.264
7E62 Mouse TAB2 NZF in complex with Lys6-linked diubiquitin Deposited 2021-02-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–76（76 aa） Chain I 1–77（77 aa）	Mutation：K6R Mutation：A77D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM HEPES-NaOH (pH 7.5), 1.44 M sodium citrate	Resolution 1.99 Å R-free 0.264
7LS1 80S ribosome from mouse bound to eEF2 (Class II) Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain U3 1–156（156 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 second blotting, force 3	Resolution 3.30 Å
7LS2 80S ribosome from mouse bound to eEF2 (Class I) Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain U3 1–156（156 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 second blotting, force 3	Resolution 3.10 Å
9QOH Mouse Ribosome POST translocation state Deposited 2025-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric	Chain U3 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 122 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9QQL Mouse RPS15 P131 Mutant Ribosome POST translocation state Deposited 2025-04-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain U3 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 122 UNK UNKNOWN × 22 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9QZP Mouse Ribosome Classical Pre translocation state Deposited 2025-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 85-meric	Chain U3 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 118 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å

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

View Construct and Data Evidence

UniProt name	RS27A_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–76； UniProt 1–76

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	3vht
Deposition date deposition_date	2011-09-06
Structure title title	Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin
Keywords keywords	GREEN FLUORESCENT PROTEIN, FUSION PROTEIN, ZINC FINGER, UBIQUITIN-BINDING DOMAIN, FLUORESCENT PROTEIN-PROTEIN BINDING complex; FLUORESCENT PROTEIN/PROTEIN BINDING
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	26.98 Å
Radius of gyration Rg (electron density) rg_electron	26.20 Å
Forward intensity I(0) i0	66789400.00
Molecular weight molecular_weight	63861.0 kDa
Excluded volume excluded_volume	79845 Å³
Envelope volume envelope_volume	96941 Å³
Hydration-shell volume shell_volume	31128 Å³
Envelope diameter envelope_diameter	97.8 Å
Shell Rg shell_rg	33.07 Å
Envelope Rg envelope_rg	26.52 Å
Shape Rg shape_rg	26.16 Å
Total Rg total_rg	27.05 Å
Total atoms total_atoms	4498
Residues n_residues	563
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	94.8 Å
Rg (real space) rg_real	27.02 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	6.6790e+07
I(0) uncertainty (real space) i0_real_error	7.4210e+05
Rg (reciprocal space) rg_reciprocal	27.01 Å
I(0) (reciprocal space) i0_reciprocal	66790000.0000
Solution quality estimate total_estimate	0.8512
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.5 Å
Skewness Skewness skewness	0.448
Kurtosis Kurtosis kurtosis	-0.071
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19470000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.918

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Green fluorescent protein
Molecular weight formula_weight	26306.6 kDa
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	4631

GSHMSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFXVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGS

来源 Source

来源生物 organism	Aequorea victoria
通用名 common_name	Jellyfish
NCBI Class编号 ncbi_taxonomy_id	6100
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Green fluorescent protein,ATPase WRNIP1
Molecular weight formula_weight	30543.5 kDa
EC 编号 ec_number	3.6.1.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFXVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGSDPFLSQLHQVQCPVCQQMMPAAHINSHLDRCLLLHPAG

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 3 Entity 3 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3vhta1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.1 — Fluorescent proteins

Domain ID domain_id	d3vhta2
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

Domain ID domain_id	d3vhtc_
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

CATH v4.4 (4 domains)

Domain ID domain_id	3vhtA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	3vhtB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	3vhtB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	3vhtC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	88.950 Å
Unit-cell length b length_b	143.692 Å
Unit-cell length c length_c	106.864 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1935
R_work r_work	0.1911
R_free r_free	0.2377

fit	/app/data/saxs_computation/vh/3vht/3vht.fit
pddf	/app/data/pr_computation/vh/3vht/3vht.pr.out
profile	/app/data/saxs_computation/vh/3vht/3vht.dat

Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin

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

Green fluorescent protein,ATPase WRNIP1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)