SAXSdb — 2yfw

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

HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4

KLUYVEROMYCES LACTIS NRRL Y-1140

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 93–184 Chain G； UniProt 93–184	Fragment：HISTONE-FOLD DOMAIN, RESIDUES 93-184	HISTONE H4 × 2 （Q6CMU6）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.1 M TRIS-HCL, PH8.5, 0.2 M NACL, AND 25% PEG 3350	Resolution 2.60 Å R-free 0.276
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 93–184 Chain E； UniProt 93–184	Fragment：HISTONE-FOLD DOMAIN, RESIDUES 93-184	HISTONE H4 × 2 （Q6CMU6）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.1 M TRIS-HCL, PH8.5, 0.2 M NACL, AND 25% PEG 3350	Resolution 2.60 Å R-free 0.276

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 2YFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YFV The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4 Deposited 2011-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 81–180（100 aa） Fragment：RESIDUES 81-180	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M SODIUM CITRATE, PH4.5, 6% PEG 4000, AND 0.1 M SODIUM IODIDE	Resolution 2.32 Å R-free 0.257

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CENPA_KLULA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–92； UniProt 93–184 Author chain C； PDBConstruct 1–92； UniProt 93–184 Author chain E； PDBConstruct 1–92； UniProt 93–184 Author chain G； PDBConstruct 1–92； UniProt 93–184

HISTONE H4

KLUYVEROMYCES LACTIS NRRL Y-1140

UniProt Q6CMU6

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–103 Chain H； UniProt 1–103	Not recorded	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 × 2 （Q6CTI2）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.1 M TRIS-HCL, PH8.5, 0.2 M NACL, AND 25% PEG 3350	Resolution 2.60 Å R-free 0.276
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–103 Chain F； UniProt 1–103	Not recorded	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 × 2 （Q6CTI2）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.1 M TRIS-HCL, PH8.5, 0.2 M NACL, AND 25% PEG 3350	Resolution 2.60 Å R-free 0.276

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 2YFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YFV The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4 Deposited 2011-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–98（74 aa） Fragment：RESIDUES 25-98	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M SODIUM CITRATE, PH4.5, 6% PEG 4000, AND 0.1 M SODIUM IODIDE	Resolution 2.32 Å R-free 0.257
6UPH Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution Deposited 2019-10-17	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6CMU6_KLULA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain D； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103 Author chain H； PDBConstruct 1–103； UniProt 1–103

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	2yfw
Deposition date deposition_date	2011-04-08
Structure title title	Heterotetramer structure of Kluyveromyces lactis Cse4,H4
Keywords keywords	CELL CYCLE, KINETOCHORE, CENTROMERE, HISTONE CHAPERONE, BUDDING YEAST; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.15 Å
Radius of gyration Rg (electron density) rg_electron	26.06 Å
Forward intensity I(0) i0	74337600.00
Molecular weight molecular_weight	68448.0 kDa
Excluded volume excluded_volume	86745 Å³
Envelope volume envelope_volume	108430 Å³
Hydration-shell volume shell_volume	33730 Å³
Envelope diameter envelope_diameter	85.6 Å
Shell Rg shell_rg	34.26 Å
Envelope Rg envelope_rg	25.85 Å
Shape Rg shape_rg	25.98 Å
Total Rg total_rg	27.25 Å
Total atoms total_atoms	4808
Residues n_residues	604
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	80.8 Å
Rg (real space) rg_real	26.96 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	7.4340e+07
I(0) uncertainty (real space) i0_real_error	8.9180e+05
Rg (reciprocal space) rg_reciprocal	27.02 Å
I(0) (reciprocal space) i0_reciprocal	74340000.0000
Solution quality estimate total_estimate	0.9131
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.077
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14830000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
Molecular weight formula_weight	10746.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	4822

ALAEIRKYQRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRGQFI

来源 Source

来源生物 organism	KLUYVEROMYCES LACTIS NRRL Y-1140
NCBI Class编号 ncbi_taxonomy_id	284590
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	HISTONE H4
Molecular weight formula_weight	11436.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

来源 Source

来源生物 organism	KLUYVEROMYCES LACTIS NRRL Y-1140
NCBI Class编号 ncbi_taxonomy_id	284590
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2yfwa_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwb_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwc_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwd_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwe_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwf_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwg_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d2yfwh_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

CATH v4.4 (8 domains)

Domain ID domain_id	2yfwA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	2yfwH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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8. Citations (1)

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Unit-cell length a length_a	169.479 Å
Unit-cell length b length_b	169.479 Å
Unit-cell length c length_c	81.215 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2211
R_work r_work	0.2183
R_free r_free	0.2763

fit	/app/data/saxs_computation/yf/2yfw/2yfw.fit
pddf	/app/data/pr_computation/yf/2yfw/2yfw.pr.out
profile	/app/data/saxs_computation/yf/2yfw/2yfw.dat

Heterotetramer structure of Kluyveromyces lactis Cse4,H4

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

HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4

State in the Current Structure

Other States of the Same Protein in the Database

HISTONE H4

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)