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2m13

The ZZ domain of cytoplasmic polyadenylation element binding protein 1 (CPEB1)

Method: SOLUTION NMR Dmax: 59.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytoplasmic polyadenylation element-binding protein 1

Homo sapiens

UniProt Q9BZB8

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 504–566 Fragment：ZZ domain of CPEB1 ZN ZINC ION × 2 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition：0.3 mM [U-100% 13C; U-100% 15N] CPEB1-ZZ G-P-504, 20 mM TRIS, 200 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM [U-100% 13C; U-100% 15N] CPEB1-ZZ T498S, 50 mM potassium phosphate, 200 mM potassium chloride, 5 mM DTT, 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 2M13 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MKE Solution structure of CPEB1 ZZ domain in the free state Deposited 2014-02-06 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 426–486（61 aa） Fragment：UNP residues 426-486
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1ZZ-1, 0.4-0.6 mM [U-100% 15N] CPEB1ZZ-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MKH Solution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in free state Deposited 2014-02-07 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 219–434（216 aa） Fragment：UNP residues 219-434
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 100 mM sodium chloride-1, 1 mM DTT-2, 1 mM magnesium sulphate-3, 50 mM sodium phosphate-4, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MKK Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA Deposited 2014-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 219–430（212 aa） Fragment：UNP residues 219-430
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；313 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-13, 0.4-0.6 mM 5'-UUUUA-3'-14, 100 mM sodium chloride-15, 50 mM sodium phosphate-16, 1 mM DTT-17, 1 mM magnesium sulfate-18, 100% D2O | 100% D2O
NMR sample composition 0.4-0.6 mM [U-100% 15N] CPEB1RRM12-19, 0.4-0.6 mM 5'-UUUUA-3'-20, 100 mM sodium chloride-21, 50 mM sodium phosphate-22, 1 mM DTT-23, 1 mM magnesium sulfate-24, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.6 mM [U-100% 15N] CPEB1RRM12-25, 0.4-0.6 mM 5'-UUUUA-3'-26, 100 mM sodium chloride-27, 50 mM sodium phosphate-28, 1 mM DTT-29, 1 mM magnesium sulfate-30, 100% D2O | 100% D2O
NMR sample composition 0.4-0.6 mM [U-100% 15N] CPEB1RRM12-31, 0.4-0.6 mM 5'-CUUUA-3'-32, 100 mM sodium chloride-33, 50 mM sodium phosphate-34, 1 mM DTT-35, 1 mM magnesium sulfate-36, 100% D2O | 100% D2O
NMR sample composition 0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-37, 0.4-0.6 mM 5'-CUUUA-3'-38, 100 mM sodium chloride-39, 50 mM sodium phosphate-40, 1 mM DTT-41, 1 mM magnesium sulfate-42, 100% D2O | 100% D2O
Resolution not provided
2N1O PIN1 WW domain in complex with a phosphorylated CPEB1 derived peptide Deposited 2015-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 206–213（8 aa） Fragment：UNP residues 206-213
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；285 K；Pressure ambient
NMR sample composition 1 mM Pin1, 3 mM CPEB1, 10 % [U-100% 2H] D2O, 20 mM [U-100% 2H] TRIS, 130 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPEB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–65； UniProt 504–566

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 2m13

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2m13
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2m13
Deposition date deposition_date2012-11-14
Structure title titleThe ZZ domain of cytoplasmic polyadenylation element binding protein 1 (CPEB1)
Keywords keywordsZinc-binding protein, ZZ motif, 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_guinier14.45 Å
Radius of gyration Rg (electron density) rg_electron14.15 Å
Forward intensity I(0) i0433539000.00
Molecular weight molecular_weight157430.0 kDa
Excluded volume excluded_volume189190 ų
Envelope volume envelope_volume41819 ų
Hydration-shell volume shell_volume18120 ų
Envelope diameter envelope_diameter64.8 Å
Shell Rg shell_rg26.06 Å
Envelope Rg envelope_rg20.62 Å
Shape Rg shape_rg14.16 Å
Total Rg total_rg14.49 Å
Total atoms total_atoms20800
Residues n_residues1300
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 dmax59.5 Å
Rg (real space) rg_real14.61 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real4.3350e+08
I(0) uncertainty (real space) i0_real_error5.4760e+06
Rg (reciprocal space) rg_reciprocal14.59 Å
I(0) (reciprocal space) i0_reciprocal433500000.0000
Solution quality estimate total_estimate0.7327
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary14.3 Å
Skewness Skewness skewness0.562
Kurtosis Kurtosis kurtosis-0.118
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha149700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.451; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.170; Smooth: 0.999
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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_id2m13A00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology640 — 30s Ribosomal Protein S18
Homologous superfamily homologous superfamily40 — Cytoplasmic polyadenylation element-binding protein, ZZ domain
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8. Citations (1)

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9. Files and Curves (10)