SAXSdb — 9f9a

▼

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

Crossover junction endonuclease MUS81

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease EME1 × 1 （Q96AY2） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease EME1 × 1 （Q96AY2） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease EME1 × 1 （Q96AY2） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease EME1 × 1 （Q96AY2） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUS81_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–308； UniProt 246–551 Author chain C； PDBConstruct 3–308； UniProt 246–551 Author chain E； PDBConstruct 3–308； UniProt 246–551 Author chain G； PDBConstruct 3–308； UniProt 246–551

Crossover junction endonuclease EME1

Homo sapiens

UniProt Q96AY2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease MUS81 × 1 （Q96NY9） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease MUS81 × 1 （Q96NY9） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease MUS81 × 1 （Q96NY9） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Crossover junction endonuclease MUS81 × 1 （Q96NY9） 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid × 1 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EME1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–326； UniProt 246–570 Author chain D； PDBConstruct 2–326； UniProt 246–570 Author chain F； PDBConstruct 2–326； UniProt 246–570 Author chain H； PDBConstruct 2–326； UniProt 246–570

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9f9a
Deposition date deposition_date	2024-05-07
Structure title title	Crystal structure of MUS81-EME1 bound by compound 12.
Keywords keywords	MUS81-EME1, fragment, inhibitor, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9f9a__assembly_1__model_1

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

Download this curve (.dat)

9f9a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9f9a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.81 Å
Rg (electron density)	20.62 Å
Total Rg	21.51 Å
Atom count	2512
Residues	323
Excluded volume	44854 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9f9a__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9f9a__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9f9a__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9f9a__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Crossover junction endonuclease MUS81
Molecular weight formula_weight	34159.9 kDa
EC 编号 ec_number	3.1.22.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	10093

GSSAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTVRKLHVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCGLERRVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQRLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFARQLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSYGPLT

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Crossover junction endonuclease EME1
Molecular weight formula_weight	36144.2 kDa
EC 编号 ec_number	3.1.22.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

GEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSEDREDWVEEPTVLVLLRAEAFVSMIDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSAQNPPRRGKQGANKQTKKQQQRQPEASIGSMVSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLALVWRRQIQQLNRVSLEMASAVVNAYPSPQLLVQAYQQCFSDKERQNLLADIQVRRGEGVTSTSRRIGPELSRRIYLQMTTLQPHLSLDSAD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

▶

Unit-cell length a length_a	111.869 Å
Unit-cell length b length_b	124.348 Å
Unit-cell length c length_c	217.571 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.911 Å
Low-resolution limit resolution_low	83.166 Å
R factor r_factor	0.2447
R_work r_work	0.2429
R_free r_free	0.2782

Crystal structure of MUS81-EME1 bound by compound 12.

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

Crossover junction endonuclease MUS81

State in the Current Structure

Other States of the Same Protein in the Database

Crossover junction endonuclease EME1

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

9f9a__assembly_1__model_1

9f9a__assembly_1__model_1 | I(q)

9f9a__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

Crystal structure of MUS81-EME1 bound by compound 12.

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

Crossover junction endonuclease MUS81

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Crossover junction endonuclease EME1

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

9f9a__assembly_1__model_1

9f9a__assembly_1__model_1 | I(q)

9f9a__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)