SAXSdb — 9y4c

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1. Structure Basics

entry_id	9y4c
deposition_date	2025-09-03
title	Strand displacement state I of Human mitochondrial DNA polymerase gamma ternary complex
keywords	DNA polymerase gamma, strand displacement, mitochondria, TRANSFERASE-DNA complex; TRANSFERASE/DNA
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	43.22 Å
rg_electron	42.97 Å
i0	789266000.00
molecular_weight	218800.0 kDa
excluded_volume	268650 Å³
envelope_volume	401120 Å³
shell_volume	76441 Å³
envelope_diameter	157.9 Å
shell_rg	49.14 Å
envelope_rg	42.41 Å
shape_rg	42.99 Å
total_rg	43.21 Å
total_atoms	15330
n_residues	1813
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	143.6 Å
rg_real	43.19 Å
rg_real_error	1.22 Å
i0_real	7.8930e+08
i0_real_error	1.3630e+07
rg_reciprocal	43.22 Å
i0_reciprocal	789300000.0000
total_estimate	0.8752
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.4 Å
skewness	0.361
kurtosis	-0.240
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	164500000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.811

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DNA polymerase subunit gamma-1
formula_weight	139628.7 kDa
ec_number	2.7.7.7
mutation	D198A, E200A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	15330

MSRLLWRKVAGATVGPGPVPAPGRWVSSSVPASDPSDGQRRRQQQQQQQQQQQQQPQQPQVLSSEGGQLRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAVPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFAVAVCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTGASSPTQRDWQEQLVVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTLESAGVVCPYRAIESLYRKHCLEQGKQQLMPQEAGLAEEFLLTDNSAIWQTVEELDYLEVEAEAKMENLRAAVPGQPLALTARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLSDEGEWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKKWEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKGSLEKRSQPGP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Insect cell expression vector pTIE1

Entity 2 polymer

description	DNA polymerase subunit gamma-2, mitochondrial
formula_weight	54991.0 kDa
ec_number	2.7.7.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C

MRSRVAVRACHKVCRCLLSGFGGRVDAGQPELLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSLLSGCHPGFGPLGVELRKNLAAEWWTSVVVFREQVFPVDALHHKPGPLLPGDSAFRLVSAETLREILQDKELSKEQLVAFLENVLKTSGKLRENLLHGALEHYVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLVWFTPPRTSNQWLDFWLRHRLQWWRKFAMSPSNFSSSDCQDEEGRKGNKLYYNFPWGKELIETLWNLGDHELLHMYPGNVSKLHGRDGRKNVVPCVLSVNGDLDRGMLAYLYDSFQLTENSFTRKKNLHRKVLKLHPCLAPIKVALDVGRGPTLELRQVCQGLFNELLENGISVWPGYLETMQSSLEQLYSKYDEMSILFTVLVTETTLENGLIHLRSRDTTMKEMMHISKLKDFLIKYISSAKNV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	DNA (77-MER)
formula_weight	23791.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GCTTTTCTGGTGAAAAGCTGGTCGGCAGCGCTTGAGCAGCGGCAGCTGGTGCTGCCGCTGCTCAAGCGCTGCCGACC

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
formula_weight	491.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.230 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.23 Å
resolution_method	—
num_particles	122123

fit	/app/data/saxs_computation/y4/9y4c/9y4c.fit
pddf	/app/data/pr_computation/y4/9y4c/9y4c.pr.out
profile	/app/data/saxs_computation/y4/9y4c/9y4c.dat

Strand displacement state I of Human mitochondrial DNA polymerase gamma ternary complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)