SAXSdb — 6j2p

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

COMPASS component SPP1

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Histone H3 × 1 （P61830） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone H3 × 1 （P61830） ZINC ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone H3 × 1 （P61830） ZINC ION × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone H3 × 1 （P61830） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPP1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–123； UniProt 1–124 Author chain B； PDBConstruct 4–123； UniProt 1–124 Author chain C； PDBConstruct 4–123； UniProt 1–124 Author chain D； PDBConstruct 4–123； UniProt 1–124

Histone H3

OrganismNot specified

UniProt P61830

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	COMPASS component SPP1 × 1 （Q03012） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	COMPASS component SPP1 × 1 （Q03012） ZINC ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	COMPASS component SPP1 × 1 （Q03012） ZINC ION × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	COMPASS component SPP1 × 1 （Q03012） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–7； UniProt 2–8 Author chain F； PDBConstruct 1–7； UniProt 2–8 Author chain G； PDBConstruct 1–7； UniProt 2–8 Author chain H； PDBConstruct 1–7； UniProt 2–8

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	6j2p
Deposition date deposition_date	2019-01-02
Structure title title	Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3
Keywords keywords	Histone modification recognition, PROTEIN BINDING; PROTEIN BINDING
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.

6j2p__assembly_1__model_1

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

Download this curve (.dat)

6j2p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6j2p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.61 Å
Rg (electron density)	16.85 Å
Total Rg	17.66 Å
Atom count	849
Residues	104
Excluded volume	15077 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6j2p__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6j2p__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6j2p__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6j2p__assembly_4__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	COMPASS component SPP1
Molecular weight formula_weight	14246.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3183

SHNMSLPQWCPPHSTLKRNPTTGEDVYCICKRPDYGELMVGCDGCDDWFHFTCLHIPEQFKDLVFSFYCPYCQAGITGKNKNGEGSLPKTLWKRKCRISDCYKPCLQDSKYCSEEHGREFVND

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H3
Molecular weight formula_weight	819.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

ARTKQTA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

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Unit-cell length a length_a	81.810 Å
Unit-cell length b length_b	106.170 Å
Unit-cell length c length_c	139.830 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	42.279 Å
R factor r_factor	0.2372
R_work r_work	0.2345
R_free r_free	0.2878

Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3

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

COMPASS component SPP1

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3

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

6j2p__assembly_1__model_1

6j2p__assembly_1__model_1 | I(q)

6j2p__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3

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

COMPASS component SPP1

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 H3

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

6j2p__assembly_1__model_1

6j2p__assembly_1__model_1 | I(q)

6j2p__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)