SAXSdb — 2fmm

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

Protein EMSY

Homo sapiens

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain E； UniProt 9–139	Fragment：N-TERMINAL DOMAIN	Chromobox protein homolog 1 × 8 （P83916） SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；1.8M ammonium sulfate, 0.1M tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.243

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	EMSY_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 3–133； UniProt 9–139

Chromobox protein homolog 1

Homo sapiens

UniProt P83916

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 104–175 Chain B； UniProt 104–175 Chain C； UniProt 104–175 Chain D； UniProt 104–175	Fragment：CHROMO SHADOW DOMAIN	Protein EMSY × 2 （Q7Z589） SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；1.8M ammonium sulfate, 0.1M tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.243

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 2FMM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3F2U Crystal structure of human chromobox homolog 1 (CBX1) Deposited 2008-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–73（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% PEG 400, 0.2M CaCl2 0.1M Na Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.274
3Q6S The crystal structure of the heterochromatin protein 1 beta chromoshadow domain complexed with a peptide from Shugoshin 1 Deposited 2011-01-03	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 108–185（78 aa） Fragment：chromoshadow domain, residues 108-185 Chain D 108–185（78 aa） Fragment：chromoshadow domain, residues 108-185	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K	Resolution 1.93 Å R-free 0.229
3Q6S The crystal structure of the heterochromatin protein 1 beta chromoshadow domain complexed with a peptide from Shugoshin 1 Deposited 2011-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 108–185（78 aa） Fragment：chromoshadow domain, residues 108-185 Chain C 108–185（78 aa） Fragment：chromoshadow domain, residues 108-185	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K	Resolution 1.93 Å R-free 0.229
5T1G chromo shadow domain of CBX1 in complex with a histone peptide Deposited 2016-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 108–185（78 aa） Fragment：unp residues 108-185	Not recorded	UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5 M sodium citrate, 0.1 M HEPES	Resolution 1.90 Å R-free 0.243
6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–73（54 aa） Fragment：UNP residues 20-73	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350	Resolution 2.10 Å R-free 0.257
6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–73（54 aa） Fragment：UNP residues 20-73	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350	Resolution 2.10 Å R-free 0.257
6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–73（54 aa） Fragment：UNP residues 20-73	Mutation：Y3F, F27G	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate	Resolution 2.10 Å R-free 0.252
6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–73（54 aa） Fragment：UNP residues 20-73	Mutation：Y3F, F27G	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate	Resolution 2.10 Å R-free 0.252

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBX1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 3–74； UniProt 104–175 Author chain B； PDBConstruct 3–74； UniProt 104–175 Author chain C； PDBConstruct 3–74； UniProt 104–175 Author chain D； PDBConstruct 3–74； UniProt 104–175

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	2fmm
Deposition date deposition_date	2006-01-09
Structure title title	Crystal Structure of EMSY-HP1 complex
Keywords keywords	ENT DOMAIN, CHROMO SHADOW DOMAIN, EMSY PROTEIN, HETEROCHROMATIN PROTEIN 1, TRANSCRIPTION; TRANSCRIPTION
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	24.98 Å
Radius of gyration Rg (electron density) rg_electron	24.20 Å
Forward intensity I(0) i0	33687300.00
Molecular weight molecular_weight	43799.0 kDa
Excluded volume excluded_volume	54535 Å³
Envelope volume envelope_volume	69163 Å³
Hydration-shell volume shell_volume	24436 Å³
Envelope diameter envelope_diameter	91.3 Å
Shell Rg shell_rg	30.60 Å
Envelope Rg envelope_rg	24.76 Å
Shape Rg shape_rg	24.16 Å
Total Rg total_rg	25.11 Å
Total atoms total_atoms	3074
Residues n_residues	386
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	86.1 Å
Rg (real space) rg_real	25.01 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	3.3690e+07
I(0) uncertainty (real space) i0_real_error	5.4350e+05
Rg (reciprocal space) rg_reciprocal	25.00 Å
I(0) (reciprocal space) i0_reciprocal	33690000.0000
Solution quality estimate total_estimate	0.7873
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.373
Kurtosis Kurtosis kurtosis	-0.284
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7983000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein EMSY
Molecular weight formula_weight	14530.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	3460

GPLDLSRDECKRILRKLELEAYAGVISALRAQGDLTKEKKDLLGELSKVLSISTERHRAEVRRAVNDERLTTIAHNMSGPNSSSEWSIEGRRLVPLMPRLVPQTAFTVTANAVANAAIQHNASLPVPAETGSK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Chromobox protein homolog 1
Molecular weight formula_weight	8385.4 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

GSKEESEKPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	386

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2fmma_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

Domain ID domain_id	d2fmmb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

Domain ID domain_id	d2fmmc_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

Domain ID domain_id	d2fmmd_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

Domain ID domain_id	d2fmme1
Class class	a — All alpha proteins
Fold Fold fold	a.283 — ENT-like
Superfamily Superfamily superfamily	a.283.1 — ENT-like
Family Family family	a.283.1.1 — Emsy N terminal (ENT) domain-like

Domain ID domain_id	d2fmme2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id	2fmmA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fmmB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fmmC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fmmD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2fmmE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
Homologous superfamily homologous superfamily	40 — ENT domain

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8. Citations (1)

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Unit-cell length a length_a	143.400 Å
Unit-cell length b length_b	63.870 Å
Unit-cell length c length_c	66.640 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	16

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2430

fit	/app/data/saxs_computation/fm/2fmm/2fmm.fit
pddf	/app/data/pr_computation/fm/2fmm/2fmm.pr.out
profile	/app/data/saxs_computation/fm/2fmm/2fmm.dat

Crystal Structure of EMSY-HP1 complex

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

Protein EMSY

State in the Current Structure

Other States of the Same Protein in the Database

Chromobox protein homolog 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)