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4aco

Structure of the budding yeast Ndc10 N-terminal domain

Method: X-RAY DIFFRACTION Dmax: 80.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT A

SACCHAROMYCES CEREVISIAE

UniProt P32504

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 1–956 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.89 Å R-free 0.232

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 4ACO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric
Chain E 2–553（552 aa） Fragment：UNP residues 2-553
Mutation：Construct comprising residues 1-554 with C-terminal Strep tag No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–956（956 aa）
Not recorded MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain E 1–956（956 aa）
Chain L 1–956（956 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6GYU Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore Deposited 2018-07-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–956（956 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name CBF3A_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–956； UniProt 1–956

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 4aco

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4aco
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4aco
Deposition date deposition_date2011-12-16
Structure title titleStructure of the budding yeast Ndc10 N-terminal domain
Keywords keywordsDNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.04 Å
Radius of gyration Rg (electron density) rg_electron23.97 Å
Forward intensity I(0) i043441300.00
Molecular weight molecular_weight53478.0 kDa
Excluded volume excluded_volume67797 ų
Envelope volume envelope_volume79488 ų
Hydration-shell volume shell_volume27658 ų
Envelope diameter envelope_diameter83.2 Å
Shell Rg shell_rg31.01 Å
Envelope Rg envelope_rg24.19 Å
Shape Rg shape_rg23.96 Å
Total Rg total_rg24.83 Å
Total atoms total_atoms3793
Residues n_residues452
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 dmax80.8 Å
Rg (real space) rg_real25.00 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real4.3440e+07
I(0) uncertainty (real space) i0_real_error6.0690e+05
Rg (reciprocal space) rg_reciprocal25.01 Å
I(0) (reciprocal space) i0_reciprocal43440000.0000
Solution quality estimate total_estimate0.8966
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.337
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7522000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.990
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4acoA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily130 — Tyrosine recombinase, N-terminal domain
Domain ID domain_id4acoA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology443 — hpI Integrase; Chain A
Homologous superfamily homologous superfamily20 — Centromere DNA-binding protein complex CBF3 subunit, domain 2
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8. Citations (1)

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9. Files and Curves (10)