SAXSdb — 2mkk

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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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 219–430	Fragment：UNP residues 219-430	;RNA (5'-R(UPUPUPUP*A)-3') ; × 1	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

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 2MKK	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 oligomeric state 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 oligomeric state 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
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 oligomeric state 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
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 2–213； UniProt 219–430

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	2mkk
Deposition date deposition_date	2014-02-07
Structure title title	Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA
Keywords keywords	;CPEB1, RNA recognition motif (RRM), Cytoplasmic polyadenylation, Protein-RNA Interaction, Translation regulation, TRANSLATION REGULATOR-RNA complex ;; TRANSLATION REGULATOR/RNA
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	18.90 Å
Radius of gyration Rg (electron density) rg_electron	18.66 Å
Forward intensity I(0) i0	917105000.00
Molecular weight molecular_weight	254040.0 kDa
Excluded volume excluded_volume	317040 Å³
Envelope volume envelope_volume	63841 Å³
Hydration-shell volume shell_volume	25021 Å³
Envelope diameter envelope_diameter	71.0 Å
Shell Rg shell_rg	28.30 Å
Envelope Rg envelope_rg	21.01 Å
Shape Rg shape_rg	18.62 Å
Total Rg total_rg	19.01 Å
Total atoms total_atoms	35320
Residues n_residues	2180
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	18.87 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	9.1710e+08
I(0) uncertainty (real space) i0_real_error	1.3610e+07
Rg (reciprocal space) rg_reciprocal	18.88 Å
I(0) (reciprocal space) i0_reciprocal	917100000.0000
Solution quality estimate total_estimate	0.8398
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.279
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3260000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Cytoplasmic polyadenylation element-binding protein 1
Molecular weight formula_weight	23930.6 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	35320

MTWSGQLPPRNYKNPIYSCKVFLGGVPWDITEAGLVNTFRVFGSLSVEWPGKDGKHPRCPPKGYVYLVFELEKSVRSLLQACSHDPLSPDGLSEYYFKMSSRRMRCKEVQVIPWVLADSNFVRSPSQRLDPSRTVFVGALHGMLNAEALAAILNDLFGGVVYAGIDTDKHKYPIGSGRVTFNNQRSYLKAVSAAFVEIKTTKFTKKVQIDPYL

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 2 Entity 2 polymer

Description description	;RNA (5'-R(UPUPUPUP*A)-3') ;
Molecular weight formula_weight	1508.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

UUUUA

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2mkkA02
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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fit	/app/data/saxs_computation/mk/2mkk/2mkk.fit
pddf	/app/data/pr_computation/mk/2mkk/2mkk.pr.out
profile	/app/data/saxs_computation/mk/2mkk/2mkk.dat

Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)