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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HISTONE H4 × 1 （Q6CMU6） SCM3 × 1 （Q6CL77） IODIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 × 1 （Q6CTI2） SCM3 × 1 （Q6CL77） IODIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 × 1 （Q6CTI2） HISTONE H4 × 1 （Q6CMU6） IODIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2yfv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2yfv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yfv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.27 Å
Rg (electron density)	19.64 Å
Total Rg	20.53 Å
Atom count	1638
Residues	202
Excluded volume	29524 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yfv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	KLUYVEROMYCES LACTIS NRRL Y-1140
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism 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

Source Source

Source organism organism	KLUYVEROMYCES LACTIS NRRL Y-1140
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism 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

Source Source

Source organism organism	KLUYVEROMYCES LACTIS NRRL Y-1140
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yfv__assembly_1__model_1

2yfv__assembly_1__model_1 | I(q)

2yfv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HISTONE H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SCM3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yfv__assembly_1__model_1

2yfv__assembly_1__model_1 | I(q)

2yfv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)