← Back to search
2yb8

Crystal structure of Nurf55 in complex with Su(z)12

Method: X-RAY DIFFRACTION Dmax: 69.2 Å Quality: GOOD
▼

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

POLYCOMB PROTEIN SU(Z)12

DROSOPHILA MELANOGASTER

UniProt Q9NJG9

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 79–91 Fragment：NURF55 BINDING EPITOPE, RESIDUES 79-91 PROBABLE HISTONE-BINDING PROTEIN CAF1 × 1 （Q24572） SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：100 MM POTASSIUM ACETATE, 2.1 M AMMONIUM SULFATE. Resolution 2.30 Å R-free 0.199

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name SUZ12_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–13； UniProt 79–91

PROBABLE HISTONE-BINDING PROTEIN CAF1

DROSOPHILA MELANOGASTER

UniProt Q24572

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–418 Fragment：RESIDUES 1-418 POLYCOMB PROTEIN SU(Z)12 × 1 （Q9NJG9） SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：100 MM POTASSIUM ACETATE, 2.1 M AMMONIUM SULFATE. Resolution 2.30 Å R-free 0.199

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 2YB8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2XYI Crystal Structure of Nurf55 in complex with a H4 peptide Deposited 2010-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–430（430 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；35%(V/V) PEG 400, 100MM MES PH 6
Resolution 1.75 Å R-free 0.195
2YBA Crystal structure of Nurf55 in complex with histone H3 Deposited 2011-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–418（418 aa） Fragment：RESIDUES 1-418
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM SODIUM CITRATE, PH 5.4; 200 MM AMMONIUM ACETATE; 23% PEG 3350.
Resolution 2.55 Å R-free 0.222
2YBA Crystal structure of Nurf55 in complex with histone H3 Deposited 2011-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–418（418 aa） Fragment：RESIDUES 1-418
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM SODIUM CITRATE, PH 5.4; 200 MM AMMONIUM ACETATE; 23% PEG 3350.
Resolution 2.55 Å R-free 0.222
3C99 Structural Basis of Histone H4 Recognition by p55 Deposited 2008-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–430（430 aa）
Not recorded CD CADMIUM ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.256
3C99 Structural Basis of Histone H4 Recognition by p55 Deposited 2008-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–430（430 aa）
Not recorded CD CADMIUM ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.256
3C9C Structural Basis of Histone H4 Recognition by p55 Deposited 2008-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–430（430 aa）
Not recorded CD CADMIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.242

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAF1_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–422； UniProt 1–418

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 2yb8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yb8
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2yb8
Deposition date deposition_date2011-03-02
Structure title titleCrystal structure of Nurf55 in complex with Su(z)12
Keywords keywordsTRANSCRIPTION, HISTONE METHLYATION, CHROMATIN REMODELLING, P55, RBBP4, RBBP7, RBAP46, RBAP48, PRC2, H4, H3K27, H3K4, WD40 DOMAIN; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier21.76 Å
Radius of gyration Rg (electron density) rg_electron20.68 Å
Forward intensity I(0) i033807700.00
Molecular weight molecular_weight43765.0 kDa
Excluded volume excluded_volume54183 ų
Envelope volume envelope_volume62522 ų
Hydration-shell volume shell_volume24557 ų
Envelope diameter envelope_diameter71.0 Å
Shell Rg shell_rg27.95 Å
Envelope Rg envelope_rg21.01 Å
Shape Rg shape_rg20.66 Å
Total Rg total_rg21.59 Å
Total atoms total_atoms3087
Residues n_residues388
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.2 Å
Rg (real space) rg_real21.64 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real3.3810e+07
I(0) uncertainty (real space) i0_real_error4.8050e+05
Rg (reciprocal space) rg_reciprocal21.66 Å
I(0) (reciprocal space) i0_reciprocal33810000.0000
Solution quality estimate total_estimate0.8955
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.8 Å
Skewness Skewness skewness0.196
Kurtosis Kurtosis kurtosis-0.412
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7521000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2yb8b_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.4 — WD40 repeat-like
Family Family familyb.69.4.1 — WD40-repeat

CATH v4.4 (1 domains)

Domain ID domain_id2yb8B00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
▶

8. Citations (1)

▶

9. Files and Curves (10)