SAXSdb — 9yi7

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

Mitochondrial genome maintenance protein MGM101

Saccharomyces cerevisiae

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–DNA Homooligomer Protein × 19 DNA 2 PDB declaration: 21-meric（21） Consistent with all polymer counts	Chain A； UniProt 23–269 Chain B； UniProt 23–269 Chain C； UniProt 23–269 Chain D； UniProt 23–269 Chain E； UniProt 23–269 Chain F； UniProt 23–269 Chain G； UniProt 23–269 Chain H； UniProt 23–269 Chain I； UniProt 23–269 Chain J； UniProt 23–269 Chain K； UniProt 23–269 Chain L； UniProt 23–269 Chain M； UniProt 23–269 Chain N； UniProt 23–269 Chain O； UniProt 23–269 Chain P； UniProt 23–269 Chain Q； UniProt 23–269 Chain R； UniProt 23–269 Chain S； UniProt 23–269	Not recorded	ssDNA (75+) × 1 ssDNA (75-) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.54 Å

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 9YI7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YI6 Cryo-EM structure of yeast Mgm101 bound to 83-mer ssDNA Deposited 2025-10-01	Different oligomeric state	Assembly 1 Protein–DNA Homooligomer；Protein × 19 PDB declaration: 20-meric	Chain A 23–269（247 aa） Chain B 23–269（247 aa） Chain C 23–269（247 aa） Chain D 23–269（247 aa） Chain E 23–269（247 aa） Chain F 23–269（247 aa） Chain G 23–269（247 aa） Chain H 23–269（247 aa） Chain I 23–269（247 aa） Chain J 23–269（247 aa） Chain K 23–269（247 aa） Chain L 23–269（247 aa） Chain M 23–269（247 aa） Chain N 23–269（247 aa） Chain O 23–269（247 aa） Chain P 23–269（247 aa） Chain Q 23–269（247 aa） Chain R 23–269（247 aa） Chain S 23–269（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
9YI8 Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA Deposited 2025-10-01	Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 19 PDB declaration: 21-meric	Chain A 23–269（247 aa） Chain B 23–269（247 aa） Chain C 23–269（247 aa） Chain D 23–269（247 aa） Chain E 23–269（247 aa） Chain F 23–269（247 aa） Chain G 23–269（247 aa） Chain H 23–269（247 aa） Chain I 23–269（247 aa） Chain J 23–269（247 aa） Chain K 23–269（247 aa） Chain L 23–269（247 aa） Chain M 23–269（247 aa） Chain N 23–269（247 aa） Chain O 23–269（247 aa） Chain P 23–269（247 aa） Chain Q 23–269（247 aa） Chain R 23–269（247 aa） Chain S 23–269（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9YI9 Cryo-EM structure of yeast Mgm101 in the lock-washer apo state Deposited 2025-10-01	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: 18-meric	Chain A 23–269（247 aa） Chain B 23–269（247 aa） Chain C 23–269（247 aa） Chain D 23–269（247 aa） Chain E 23–269（247 aa） Chain F 23–269（247 aa） Chain G 23–269（247 aa） Chain H 23–269（247 aa） Chain I 23–269（247 aa） Chain J 23–269（247 aa） Chain K 23–269（247 aa） Chain L 23–269（247 aa） Chain M 23–269（247 aa） Chain N 23–269（247 aa） Chain O 23–269（247 aa） Chain P 23–269（247 aa） Chain R 23–269（247 aa） Chain S 23–269（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9YIA Cryo-EM structure of yeast Mgm101 in the ring apo state Deposited 2025-10-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 19 PDB declaration: 19-meric	Chain A 23–269（247 aa） Chain B 23–269（247 aa） Chain C 23–269（247 aa） Chain D 23–269（247 aa） Chain E 23–269（247 aa） Chain F 23–269（247 aa） Chain G 23–269（247 aa） Chain H 23–269（247 aa） Chain I 23–269（247 aa） Chain J 23–269（247 aa） Chain K 23–269（247 aa） Chain L 23–269（247 aa） Chain M 23–269（247 aa） Chain N 23–269（247 aa） Chain O 23–269（247 aa） Chain P 23–269（247 aa） Chain Q 23–269（247 aa） Chain R 23–269（247 aa） Chain S 23–269（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MG101_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 10–256； UniProt 23–269 Author chain B； PDBConstruct 10–256； UniProt 23–269 Author chain C； PDBConstruct 10–256； UniProt 23–269 Author chain D； PDBConstruct 10–256； UniProt 23–269 Author chain E； PDBConstruct 10–256； UniProt 23–269 Author chain F； PDBConstruct 10–256； UniProt 23–269 Author chain G； PDBConstruct 10–256； UniProt 23–269 Author chain H； PDBConstruct 10–256； UniProt 23–269 Author chain I； PDBConstruct 10–256； UniProt 23–269 Author chain J； PDBConstruct 10–256； UniProt 23–269 Author chain K； PDBConstruct 10–256； UniProt 23–269 Author chain L； PDBConstruct 10–256； UniProt 23–269 Author chain M； PDBConstruct 10–256； UniProt 23–269 Author chain N； PDBConstruct 10–256； UniProt 23–269 Author chain O； PDBConstruct 10–256； UniProt 23–269 Author chain P； PDBConstruct 10–256； UniProt 23–269 Author chain Q； PDBConstruct 10–256； UniProt 23–269 Author chain R； PDBConstruct 10–256； UniProt 23–269 Author chain S； PDBConstruct 10–256； UniProt 23–269

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	9yi7
Deposition date deposition_date	2025-10-01
Structure title title	Cryo-EM structure of yeast Mgm101 bound to duplex DNA annealing intermediate
Keywords keywords	Single strand annealing protein, SSAP, annealase, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	ELECTRON MICROSCOPY

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

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ssDNA (75+)
Molecular weight formula_weight	13642.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y
Atom count atom_count	30704

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Entity 2 Entity 2 polymer

Description description	ssDNA (75-)
Molecular weight formula_weight	13822.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Z

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Entity 3 Entity 3 polymer

Description description	Mitochondrial genome maintenance protein MGM101
Molecular weight formula_weight	28524.5 kDa
Source method src_method	man
Copy count entity_count	19

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,B,D,F,H,I,J,K,L,M,N,O,P,Q,R,S

GPKVPEFGSVVSTGTSNTATAGAVRKSFNSTETKPVFATKSEAGNGSHMKEYSSGINSKLGGTPLETRSTADDSLNNSYKQVKGDIDWYTSWYGLGMKPFEAKVQKDLIEPLDPKDIEIKPDGLIYLPEIKYRRILNKAFGAGGWGLVPRSQTIVTSKLVTREYGLICHGQLISVARGEQDYFNEAGIPTATEGCKSNALMRCCKDLGVGSELWDPVFIKKFKVDHCTEKFVEHVTTKRKKKIWLRKDRQVEYPYK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.540 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.54 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	40943

Cryo-EM structure of yeast Mgm101 bound to duplex DNA annealing intermediate

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

Mitochondrial genome maintenance protein MGM101

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (0)