SAXSdb — 2yfv

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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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 81–180	Fragment：RESIDUES 81-180	HISTONE H4 × 1 （Q6CMU6） SCM3 × 1 （Q6CL77） 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

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 2YFV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YFW Heterotetramer structure of Kluyveromyces lactis Cse4,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 × 4 PDB declaration: tetrameric	Chain A 93–184（92 aa） Fragment：HISTONE-FOLD DOMAIN, RESIDUES 93-184 Chain G 93–184（92 aa） Fragment：HISTONE-FOLD DOMAIN, RESIDUES 93-184	Not recorded	No recorded non-water small molecule	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
2YFW Heterotetramer structure of Kluyveromyces lactis Cse4,H4 Deposited 2011-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 93–184（92 aa） Fragment：HISTONE-FOLD DOMAIN, RESIDUES 93-184 Chain E 93–184（92 aa） Fragment：HISTONE-FOLD DOMAIN, RESIDUES 93-184	Not recorded	No recorded non-water small molecule	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

1 other PDB entries and 2 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 1–100； UniProt 81–180

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 25–98	Fragment：RESIDUES 25-98	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 × 1 （Q6CTI2） SCM3 × 1 （Q6CL77） 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

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 2YFV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YFW Heterotetramer structure of Kluyveromyces lactis Cse4,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 × 4 PDB declaration: tetrameric	Chain B 1–103（103 aa） Chain H 1–103（103 aa）	Not recorded	No recorded non-water small molecule	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
2YFW Heterotetramer structure of Kluyveromyces lactis Cse4,H4 Deposited 2011-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	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
6UPH Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution Deposited 2019-10-17	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 × 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 3 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 1–74； UniProt 25–98

SCM3

KLUYVEROMYCES LACTIS NRRL Y-1140

UniProt Q6CL77

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 41–103	Fragment：RESIDUES 41-103	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 × 1 （Q6CTI2） HISTONE H4 × 1 （Q6CMU6） 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

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	Q6CL77_KLULA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–63； UniProt 41–103

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	2yfv
Deposition date deposition_date	2011-04-08
Structure title title	The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and 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	20.27 Å
Radius of gyration Rg (electron density) rg_electron	19.64 Å
Forward intensity I(0) i0	10361300.00
Molecular weight molecular_weight	23582.0 kDa
Excluded volume excluded_volume	29524 Å³
Envelope volume envelope_volume	36192 Å³
Hydration-shell volume shell_volume	16482 Å³
Envelope diameter envelope_diameter	73.2 Å
Shell Rg shell_rg	24.65 Å
Envelope Rg envelope_rg	20.19 Å
Shape Rg shape_rg	19.61 Å
Total Rg total_rg	20.53 Å
Total atoms total_atoms	1638
Residues n_residues	202
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	70.5 Å
Rg (real space) rg_real	20.35 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.0360e+07
I(0) uncertainty (real space) i0_real_error	1.1890e+05
Rg (reciprocal space) rg_reciprocal	20.33 Å
I(0) (reciprocal space) i0_reciprocal	10360000.0000
Solution quality estimate total_estimate	0.7801
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.5 Å
Skewness Skewness skewness	0.501
Kurtosis Kurtosis kurtosis	-0.068
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1758000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
Molecular weight formula_weight	11692.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1696

KARGTRYKPTDLALAEIRKYQRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIR

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	8456.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTL

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 polymer

Description description	SCM3
Molecular weight formula_weight	7430.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

RDGVVYIMSKENRLIPKLSDEEVMERHKKADENMKRVWSQIIQKYESIDNQGDVIDLQTGEVI

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 4 Entity 4 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2yfva_
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	d2yfvb_
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 (3 domains)

Domain ID domain_id	2yfvA00
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	2yfvB00
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	2yfvC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2010 —

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8. Citations (1)

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Unit-cell length a length_a	32.723 Å
Unit-cell length b length_b	65.530 Å
Unit-cell length c length_c	121.097 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.320 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2220
R_work r_work	0.2203
R_free r_free	0.2571

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

The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and 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

SCM3

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)