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4kr1

Crystal structure of the kinetechore protein Iml3 from budding yeast

Method: X-RAY DIFFRACTION Dmax: 64.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Central kinetochore subunit IML3

Saccharomyces cerevisiae

UniProt P38265

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 1–245 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；3M Sodium formate, 100mM Cesium chloride, 3% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K Resolution 2.50 Å R-free 0.262

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 4KR1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4IT3 Crystal Structure of Iml3 from S. cerevisiae Deposited 2013-01-17 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–245（245 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；3.75 M sodium formate, 4% 2,5-diaminopentane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.256
4JE3 An Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation Deposited 2013-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–242（242 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.35 M lithium citrate, pH 9, 25% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.28 Å R-free 0.211
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLD Structure of inner kinetochore CCAN-Cenp-A complex Deposited 2019-01-31 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain L 2–242（241 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.15 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain L 1–245（245 aa）
Chain LL 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IML3_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–247； UniProt 1–245

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 4kr1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4kr1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4kr1
Deposition date deposition_date2013-05-16
Structure title titleCrystal structure of the kinetechore protein Iml3 from budding yeast
Keywords keywordschromosome segregation, kinetochore protein, CELL CYCLE; CELL CYCLE
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_guinier19.25 Å
Radius of gyration Rg (electron density) rg_electron18.23 Å
Forward intensity I(0) i010332600.00
Molecular weight molecular_weight24229.0 kDa
Excluded volume excluded_volume30329 ų
Envelope volume envelope_volume35457 ų
Hydration-shell volume shell_volume16754 ų
Envelope diameter envelope_diameter65.5 Å
Shell Rg shell_rg23.87 Å
Envelope Rg envelope_rg18.51 Å
Shape Rg shape_rg18.28 Å
Total Rg total_rg18.98 Å
Total atoms total_atoms1675
Residues n_residues210
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 dmax64.5 Å
Rg (real space) rg_real19.23 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real1.0330e+07
I(0) uncertainty (real space) i0_real_error1.4330e+05
Rg (reciprocal space) rg_reciprocal19.24 Å
I(0) (reciprocal space) i0_reciprocal10330000.0000
Solution quality estimate total_estimate0.7967
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.356
Kurtosis Kurtosis kurtosis-0.249
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2395000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.793; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000
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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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8. Citations (1)

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9. Files and Curves (10)