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9r96

;Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA (pppGpGpA) and GTP poised for catalysis (slipped pre-IC4) ;

Method: ELECTRON MICROSCOPY D_max: 136.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r96
deposition_date	2025-05-19
title	;Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA (pppGpGpA) and GTP poised for catalysis (slipped pre-IC4) ;
keywords	;POLRMT, TFB2M, TFAM, transcription, initiation, transcription initiation, polymerase, h-mtRNAP, y-mtRNAP, mtRNAP, RNA, DNA, RNAP, RNA polymerase, mitochondria, mitochondrial DNA, slippage ;; TRANSCRIPTION
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	42.93 Å
rg_electron	42.44 Å
i0	786699000.00
molecular_weight	209520.0 kDa
excluded_volume	253780 Å³
envelope_volume	385800 Å³
shell_volume	75466 Å³
envelope_diameter	138.5 Å
shell_rg	48.20 Å
envelope_rg	41.39 Å
shape_rg	42.44 Å
total_rg	42.71 Å
total_atoms	14595
n_residues	1669
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	136.4 Å
rg_real	42.82 Å
rg_real_error	1.38 Å
i0_real	7.8670e+08
i0_real_error	1.3410e+07
rg_reciprocal	42.93 Å
i0_reciprocal	786800000.0000
total_estimate	0.8918
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.6 Å
skewness	0.243
kurtosis	-0.481
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	85560000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.831

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	DNA-directed RNA polymerase, mitochondrial
formula_weight	134632.3 kDa
ec_number	2.7.7.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14606

SASPQEQDQDRRKDWGHVELLEVLQARVRQLQAESVSEVVVNRVDVARLPECGSGDGSLQPPRKVQMGAKDATPVPCGRWAKILEKDKRTQQMRMQRLKAKLQMPFQSGEFKALTRRLQVEPRLLSKQMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQLHMELASRVCVVSVEKPTLPSKEVKHARKTLKTLRDQWEKALCRALRETKNRLEREVYEGRFSLYPFLCLLDEREVVRMLLQVLQALPAQGESFTTLARELSARTFSRHVVQRQRVSGQVQALQNHYRKYLCLLASDAEVPEPCLPRQYWEELGAPEALREQPWPLPVQMELGKLLAEMLVQATQMPCSLDKPHRSSRLVPVLYHVYSFRNVQQIGILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTKLMRTVEGATQHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQLFQAKGCPQLGVPAPPSEAPQPPEAHLPHSAAPARKAELRRELAHCQKVAREMHSLRAEALYRLSLAQHLRDRVFWLPHNMDFRGRTYPCPPHFNHLGSDVARALLEFAQGRPLGPHGLDWLKIHLVNLTGLKKREPLRKRLAFAEEVMDDILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAVRASDPAAYVSHLPVHQDGSCNGLQHYAALGRDSVGAASVNLEPSDVPQDVYSGVAAQVEVFRRQDAQRGMRVAQVLEGFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRELSDFPQEFVWEASHYLVRQVFKSLQEMFSGTRAIQHWLTESARLISHMGSVVEWVTPLGVPVIQPYRLDSKVKQIGGGIQSITYTHNGDISRKPNTRKQKNGFPPNFIHSLDSSHMMLTALHCYRKGLTFVSVHDCYWTHAADVSVMNQVCREQFVRLHSEPILQDLSRFLVKRFCSEPQKILEASQLKETLQAVPKPGAFDLEQVKRSTYFFS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 polymer

description	Non-template strand DNA (56-MER)
formula_weight	17486.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	N

ATGTGTTAGTTGGGGGGTGACTGTTAAAAGTGCATACCGAACAAAGATAAAATTTG

Entity 3 polymer

description	template strand DNA (56-MER)
formula_weight	17023.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CAAATTTTATCTCCAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACAT

Entity 4 polymer

description	Dimethyladenosine transferase 2, mitochondrial
formula_weight	38901.3 kDa
ec_number	2.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

PPRKASKASLDFKRYVTDRRLAETLAQIYLGKPSRPPHLLLECNPGPGILTQALLEAGAKVVALESDKTFIPHLESLGKNLDGKLRVIHCDFFKLDPRSGGVIKPPAMSSRGLFKNLGIEAVPWTADIPLKVVGMFPSRGEKRALWKLAYDLYSCTSIYKFGRIEVNMFIGEKEFQKLMADPGNPDLYHVLSVIWQLACEIKVLHMEPWSSFDIYTRKGPLENPKRRELLDQLQQKLYLIQMIPRQNLFTKNLTPMNYNIFFHLLKHCFGRRSATVIDHLRSLTPLDARDILMQIGKQEDEKVVNMHPQDFKTLFETIERSKDCAYKWLYDETLEDR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli B

Entity 5 polymer

description	;RNA (5'-D((GTP))-R(PGP*(3DA))-3') ;
formula_weight	1118.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	R

GGA

Entity 6 polymer

description	Transcription factor A, mitochondrial
formula_weight	27637.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSYYHHHHHHDYDIPTTENLYFQGAMGSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 7 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 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	3.10 Å
resolution_method	—
num_particles	155000

fit	/app/data/saxs_computation/r9/9r96/9r96.fit
pddf	/app/data/pr_computation/r9/9r96/9r96.pr.out
profile	/app/data/saxs_computation/r9/9r96/9r96.dat

;Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA (pppGpGpA) and GTP poised for catalysis (slipped pre-IC4) ;

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)