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2kzy

Solution NMR structure of the ZNF216 A20 zinc finger

Method: SOLUTION NMR Dmax: 48.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a)

Rattus norvegicus

UniProt B5DF11

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 1–60 Fragment：A20 ZN ZINC ION × 1 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：1 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1.2 mM [U-100% 15N] ZNF216-A20-6, 50 uM Zinc-7, 0.1 mM DSS-8, 5 mM TRIS-9, 50 mM sodium chloride-10, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-11, 50 uM Zinc-12, 0.1 mM DSS-13, 5 mM TRIS-14, 50 mM sodium chloride-15, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1.2 mM [U-100% 15N] ZNF216-A20-16, 50 uM Zinc-17, 0.1 mM DSS-18, 5 mM TRIS-19, 50 mM sodium chloride-20, 7 % Polyacrylamide gel-21, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2KZY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2L00 Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin Deposited 2010-06-29 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–60（60 aa） Fragment：A20
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 4 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 1 mM [U-100% 15N] ubiquitin-6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-7, 50 uM Zinc-8, 4 mM MTSL-9, 5 mM TRIS-10, 50 mM sodium chloride-11, 4 mM ubiquitin-12, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-13, 50 uM Zinc-14, 0.1 mM DSS-15, 5 mM TRIS-16, 50 mM sodium chloride-17, 2 mM ubiquitin-18, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-19, 50 uM Zinc-20, 0.1 mM DSS-21, 5 mM TRIS-22, 50 mM sodium chloride-23, 5 % Polyacrylamide gel-24, 4 mM ubiquitin-25, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM ZNF216-A20-26, 50 uM Zinc-27, 0.1 mM DSS-28, 5 mM TRIS-29, 50 mM sodium chloride-30, 5 % Polyacrylamide gel-31, 1 mM [U-100% 15N] ubiquitin-32, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mM ZNF216-A20-33, 50 uM Zinc-34, 0.1 mM DSS-35, 5 mM TRIS-36, 50 mM sodium chloride-37, 1 mM [U-100% 13C; U-100% 15N] ubiquitin-38, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] ZNF216-A20-39, 50 uM Zinc-40, 0.1 mM DSS-41, 5 mM TRIS-42, 50 mM sodium chloride-43, 4 mM ubiquitin-44, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name B5DF11_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–62； UniProt 1–60

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 2kzy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2kzy
Deposition date deposition_date2010-06-28
Structure title titleSolution NMR structure of the ZNF216 A20 zinc finger
Keywords keywordsA20 domain, ZNF216, Atrogene, zinc finger, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.41 Å
Radius of gyration Rg (electron density) rg_electron18.26 Å
Forward intensity I(0) i0356316000.00
Molecular weight molecular_weight132010.0 kDa
Excluded volume excluded_volume155120 ų
Envelope volume envelope_volume69722 ų
Hydration-shell volume shell_volume23809 ų
Envelope diameter envelope_diameter98.7 Å
Shell Rg shell_rg31.60 Å
Envelope Rg envelope_rg25.72 Å
Shape Rg shape_rg18.30 Å
Total Rg total_rg18.75 Å
Total atoms total_atoms17340
Residues n_residues1240
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 dmax48.3 Å
Rg (real space) rg_real16.95 Å
Rg uncertainty (real space) rg_real_error0.09 Å
I(0) (real space) i0_real3.3910e+08
I(0) uncertainty (real space) i0_real_error3.1270e+06
Rg (reciprocal space) rg_reciprocal18.77 Å
I(0) (reciprocal space) i0_reciprocal356300000.0000
Solution quality estimate total_estimate0.6697
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.2 Å
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.701
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha3.0310
Highest regularization parameter α highest_alpha60410.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.009; Oscil: 0.999; Stabil: 0.988; Sysdev: 0.000; Positv: 1.000; Valcen: 0.750; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2kzyA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
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8. Citations (1)

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9. Files and Curves (10)