SAXSdb — 9ibz

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

DNA polymerase subunit gamma-1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	DNA polymerase subunit gamma-2 × 2 （Q9UHN1） DNA (primer strand) × 1 DNA (template strand) × 1 CALCIUM ION × 2 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q75WC0_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–1199； UniProt 26–1217

DNA polymerase subunit gamma-2

Homo sapiens

UniProt Q9UHN1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	DNA polymerase subunit gamma-1 × 1 （Q75WC0） DNA (primer strand) × 1 DNA (template strand) × 1 CALCIUM ION × 2 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOG2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–461； UniProt 26–485 Author chain C； PDBConstruct 2–461； UniProt 26–485

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	9ibz
Deposition date deposition_date	2025-02-14
Last revision last_revision	2025-06-04
Structure title title	Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in human-like error-editing conformer (composite)
Keywords keywords	Mitochondrial DNA polymerase, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

9ibz__assembly_1__model_1

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

Download this curve (.dat)

9ibz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ibz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.39 Å
Rg (electron density)	40.98 Å
Total Rg	41.31 Å
Atom count	14339
Residues	1721
Excluded volume	252070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ibz__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	DNA polymerase subunit gamma-1
Molecular weight formula_weight	135078.2 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14339

MHHHHHHVSSSVLDPVPSDGRPPSQMPSSENGQLRLNPLLIQMLSRGLHEQIFGCGGEMPDEAAVQRSVEHLQKHGLWGQPATPLPDVELRLPRLFGGNLDQHFRLLAQKQSLPYLEAAASLLEAQLPPEPKSWAWAEGWTRYGPEGEAEPVAIPEERALVFDVEVCLAEGTCPTLAVAISPSAWYSWCSRRLVEERYSWTSQLSPADLIPLGGSTSASSSTKQDGQEQLVVGHNVSFDRAHIREQYLIQDSRMRFLDTMSMHMAISGLSSFQRSLWMGAKQGKHKTQQSTKRGQKSPRKANGPAISSWDWMDISSANNLADVHNLYVGGPPLEKEPRELFVKGSMRDIRENFQDLMQYCARDVWATFEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLTEAQNTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKAKKVKKPASASKLPIEGAGPFGDPMDQEDPGPPSEEEELQRSVTAHNRLQQLRSTTDLLPKRPQHLPGHPGWYRKLCPRLDDPAWAPGPSLLSLQMRVTPKLMALTWDGFPLHYSDSHGWGYLVPGRRDNLTEPPVSPTVESAAVTCPYRAIESLYRKHCLEQGKQQLEPQEVDLAEEFLLTDSSAMWQTVEELGCLDVEAEAKMENSGLSQPLVLPAACAPKSSQPTYHHGNGPYNDVNIPGCWFFKLPHKDGNNYNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRVVTRHPSFDEEGHYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYVLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTAATVGISREHAKIFNYGRIYGAGQSFAERLLMQFNHRLTRQEAAEKAQQMYAVTKGLRRYRLSADGEWLVKQLNLPVDRTEDGWVSLQDLRMIRREASRKSRWKKWEVASERAWTGGTESEMFNKLESIAMSDTPRTPVLGCCISRALEPSVVQGEFITSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDQCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKGSLEKRSQPGP

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	DNA polymerase subunit gamma-2
Molecular weight formula_weight	53229.7 kDa
Mutation mutation	A169T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

MDAGQPELLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSLLSGCHPGFGPLGVELRKNLAAEWWTSVVVFREQVFPVDALHHKPGPLLPGDSAFRLVSAETLREILQDKELSKEQLVTFLENVLKTSGKLRENLLHGALEHYVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLVWFTPPRTSNQWLDFWLRHRLQWWRKFAMSPSNFSSSDCQDEEGRKGNKLYYNFPWGKELIETLWNLGDHELLHMYPGNVSKLHGRDGRKNVVPCVLSVNGDLDRGMLAYLYDSFQLTENSFTRKKNLHRKVLKLHPCLAPIKVALDVGRGPTLELRQVCQGLFNELLENGISVWPGYLETMQSSLEQLYSKYDEMSILFTVLVTETTLENGLIHLRSRDTTMKEMMHISKLKDFLIKYISSAKNVHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	DNA (primer strand)
Molecular weight formula_weight	7780.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

GCATGCGGTCGAGTCTAGAGGAGCT

Entity 4 Entity 4 polymer

Description description	DNA (template strand)
Molecular weight formula_weight	12162.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TTTTTTTTTTATCCGGGCTCCTCTAGACTCGACCGCATGC

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	467.2 kDa
Source method src_method	syn
Copy count entity_count	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	3.080 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.08 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	370910

Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in human-like error-editing conformer (composite)

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

DNA polymerase subunit gamma-1

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase subunit gamma-2

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

9ibz__assembly_1__model_1

9ibz__assembly_1__model_1 | I(q)

9ibz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in human-like error-editing conformer (composite)

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

DNA polymerase subunit gamma-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase subunit gamma-2

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

9ibz__assembly_1__model_1

9ibz__assembly_1__model_1 | I(q)

9ibz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)