SAXSdb — 2mkh

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

Cytoplasmic polyadenylation element-binding protein 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 219–434	Fragment：UNP residues 219-434	No other associated polymer	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

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 2MKH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M13 The ZZ domain of cytoplasmic polyadenylation element binding protein 1 (CPEB1) Deposited 2012-11-14	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 504–566（63 aa） Fragment：ZZ domain of CPEB1	Not recorded	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
2MKE Solution structure of CPEB1 ZZ domain in the free state Deposited 2014-02-06	Different construct Different ligand/ion 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
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 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 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 2–217； UniProt 219–434

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	2mkh
Deposition date deposition_date	2014-02-07
Structure title title	Solution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in free state
Keywords keywords	CPEB1, RNA recognition motif (RRM), Cytoplasmic polyadenylation, Translational regulation, TRANSLATION REGULATOR; TRANSLATION REGULATOR
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	20.39 Å
Radius of gyration Rg (electron density) rg_electron	20.03 Å
Forward intensity I(0) i0	2911450000.00
Molecular weight molecular_weight	475570.0 kDa
Excluded volume excluded_volume	601420 Å³
Envelope volume envelope_volume	58286 Å³
Hydration-shell volume shell_volume	22624 Å³
Envelope diameter envelope_diameter	77.4 Å
Shell Rg shell_rg	28.71 Å
Envelope Rg envelope_rg	22.23 Å
Shape Rg shape_rg	19.97 Å
Total Rg total_rg	20.35 Å
Total atoms total_atoms	67200
Residues n_residues	4240
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	68.4 Å
Rg (real space) rg_real	20.46 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	2.9110e+09
I(0) uncertainty (real space) i0_real_error	3.8750e+07
Rg (reciprocal space) rg_reciprocal	20.45 Å
I(0) (reciprocal space) i0_reciprocal	2911000000.0000
Solution quality estimate total_estimate	0.7935
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.385
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1751000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2mkhA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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8. Citations (1)

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Description description	Cytoplasmic polyadenylation element-binding protein 1
Molecular weight formula_weight	24375.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	67200

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

fit	/app/data/saxs_computation/mk/2mkh/2mkh.fit
pddf	/app/data/pr_computation/mk/2mkh/2mkh.pr.out
profile	/app/data/saxs_computation/mk/2mkh/2mkh.dat

Solution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in free state

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

Cytoplasmic polyadenylation element-binding protein 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)