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4je3

An Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation

Method: X-RAY DIFFRACTION Dmax: 76.8 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–242 Not recorded Central kinetochore subunit CHL4 × 1 （P38907） 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

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 4JE3 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 construct Different mutation/modification Different oligomeric state 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
4KR1 Crystal structure of the kinetechore protein Iml3 from budding yeast Deposited 2013-05-16 Different construct Different mutation/modification Different oligomeric state 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 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
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct 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 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 construct 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 construct 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 construct 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 construct 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 4–245； UniProt 1–242

Central kinetochore subunit CHL4

Saccharomyces cerevisiae

UniProt P38907

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 361–458 Fragment：UNP residues 361-458 Central kinetochore subunit IML3 × 1 （P38265） 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

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 4JE3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–458（458 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain N 5–451（447 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain N 1–458（458 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–458（458 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain N 1–458（458 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 construct 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 N 1–458（458 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 N 1–458（458 aa）
Chain NN 1–458（458 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

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHL4_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–101； UniProt 361–458

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 4je3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4je3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4je3
Deposition date deposition_date2013-02-26
Structure title titleAn Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation
Keywords keywordskinetochore, beta sheet, chromosome segregation, Iml3-Chl4 dimer, nucleus, 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_guinier23.62 Å
Radius of gyration Rg (electron density) rg_electron22.54 Å
Forward intensity I(0) i022054300.00
Molecular weight molecular_weight36466.0 kDa
Excluded volume excluded_volume45988 ų
Envelope volume envelope_volume54375 ų
Hydration-shell volume shell_volume20953 ų
Envelope diameter envelope_diameter77.9 Å
Shell Rg shell_rg28.53 Å
Envelope Rg envelope_rg22.77 Å
Shape Rg shape_rg22.56 Å
Total Rg total_rg23.29 Å
Total atoms total_atoms2565
Residues n_residues320
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 dmax76.8 Å
Rg (real space) rg_real23.65 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real2.2050e+07
I(0) uncertainty (real space) i0_real_error3.2550e+05
Rg (reciprocal space) rg_reciprocal23.65 Å
I(0) (reciprocal space) i0_reciprocal22050000.0000
Solution quality estimate total_estimate0.8947
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.2 Å
Skewness Skewness skewness0.356
Kurtosis Kurtosis kurtosis-0.467
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3821000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4je3B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily720 —
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8. Citations (1)

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9. Files and Curves (10)