SAXSdb — 2efi

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

Mortality factor 4-like protein 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–93	Fragment：Chromo domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.13mM Chromo domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2EFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AQL Crystal Structure of the MRG15 MRG domain Deposited 2005-08-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 190–362（173 aa） Chain B 190–362（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；PEG 10000, cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.273
2F5J Crystal structure of MRG domain from human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 190–362（173 aa） Fragment：MRG domain Chain B 190–362（173 aa） Fragment：MRG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；20% PEG 4000, 0.1M HEPES, 5% iso-propanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2LKM Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology Deposited 2011-10-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 194–362（169 aa） Fragment：UNP residues 194-362	Mutation：K201R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM potassium chloride, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided
2N1D Solution structure of the MRG15-MRGBP complex Deposited 2015-03-27	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 194–362（169 aa） Fragment：UNP residues 194-362	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；308 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] protein 1, 0.8 mM protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] protein 1, 0.8 mM protein 2, 100% D2O \| 100% D2O NMR sample composition 0.9 mM protein 1, 0.9 mM [U-100% 13C; U-100% 15N] protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM protein 1, 0.9 mM [U-100% 13C; U-100% 15N] protein 2, 100% D2O \| 100% D2O	Resolution not provided
6INE Crystal Structure of human ASH1L-MRG15 complex Deposited 2018-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 190–362（173 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris-HCl pH 8.5, 20 % PEG 6000, 0.2 M Trimethylamine-N-oxide	Resolution 2.60 Å R-free 0.237
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 152–323（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；Ammonium sulfate, Tris HCl	Resolution 2.69 Å R-free 0.297
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 152–323（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；Ammonium sulfate, Tris HCl	Resolution 2.69 Å R-free 0.297
8BPA Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom Deposited 2022-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–362（362 aa）	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8C60 Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution Deposited 2023-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–362（362 aa）	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MO4L1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–100； UniProt 1–93

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	2efi
Deposition date deposition_date	2007-02-22
Structure title title	Solution structure of the chromo domain of Mortality factor 4-like protein 1 from human
Keywords keywords	;Chromo domain, Mortality factor 4-like protein 1, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.16 Å
Radius of gyration Rg (electron density) rg_electron	15.73 Å
Forward intensity I(0) i0	746151000.00
Molecular weight molecular_weight	229860.0 kDa
Excluded volume excluded_volume	287210 Å³
Envelope volume envelope_volume	43671 Å³
Hydration-shell volume shell_volume	18250 Å³
Envelope diameter envelope_diameter	72.1 Å
Shell Rg shell_rg	26.77 Å
Envelope Rg envelope_rg	21.47 Å
Shape Rg shape_rg	15.64 Å
Total Rg total_rg	16.27 Å
Total atoms total_atoms	32220
Residues n_residues	2000
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	43.6 Å
Rg (real space) rg_real	15.15 Å
Rg uncertainty (real space) rg_real_error	0.08 Å
I(0) (real space) i0_real	7.1210e+08
I(0) uncertainty (real space) i0_real_error	6.0210e+06
Rg (reciprocal space) rg_reciprocal	16.31 Å
I(0) (reciprocal space) i0_reciprocal	746100000.0000
Solution quality estimate total_estimate	0.6859
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.326
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	2.9080
Highest regularization parameter α highest_alpha	269200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.986; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2efia2
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.34.13.3 — Chromo barrel domain

Domain ID domain_id	d2efia3
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 (1 domains)

Domain ID domain_id	2efiA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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8. Citations (1)

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Description description	Mortality factor 4-like protein 1
Molecular weight formula_weight	11524.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	32220

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/ef/2efi/2efi.fit
pddf	/app/data/pr_computation/ef/2efi/2efi.pr.out
profile	/app/data/saxs_computation/ef/2efi/2efi.dat

Solution structure of the chromo domain of Mortality factor 4-like protein 1 from human

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

Mortality factor 4-like protein 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)