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9x1m

The cryo-EM structure of HerA-NurA complex with AMPPNP and dsDNA from Thermococcus kodakarensis

Method: ELECTRON MICROSCOPY D_max: 170.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x1m
deposition_date	2025-10-02
title	The cryo-EM structure of HerA-NurA complex with AMPPNP and dsDNA from Thermococcus kodakarensis
keywords	HerA, Helicase, NurA, Nuclease, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	51.95 Å
rg_electron	51.55 Å
i0	3520370000.00
molecular_weight	492440.0 kDa
excluded_volume	614560 Å³
envelope_volume	849160 Å³
shell_volume	131040 Å³
envelope_diameter	173.3 Å
shell_rg	60.02 Å
envelope_rg	50.32 Å
shape_rg	51.58 Å
total_rg	51.66 Å
total_atoms	34604
n_residues	4300
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	170.1 Å
rg_real	51.79 Å
rg_real_error	1.07 Å
i0_real	3.5200e+09
i0_real_error	6.1340e+07
rg_reciprocal	52.07 Å
i0_reciprocal	3522000000.0000
total_estimate	0.8688
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	62.4 Å
skewness	0.252
kurtosis	-0.345
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	525100000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.797

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DNA helicase
formula_weight	66118.1 kDa
ec_number	3.6.4.12
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	34604

MRIAEDINKPVGIVTGEATVSSFQFYAHPDTDLKFGDFVVARLCKEAKDQNCRWGENEEGVEWVIGTIRGLKNINWLLSEGKSTYTSLELDIREYGESIGENEALIVTVHVLGKVQLNGEKAEVVPTRVPVPNGNRVYLASSDLLRAIYYGGNGYIELGRLIIREDVPVYLNVNELVSRHFAILAVTGAGKSNTVSVMLWKLVEELGGTVIVLDPHGDYTKLSLPGTGREYVNLIEAKIRPEAMDGEELADLMEIQSNASIQRSYLLRAWDTVLHENQGIGGREAVKLVHDLLQRWASEGGGTYWDPHAGQYRDLGEIKSAEKETIMRLTMKVSRFLRNYGHLLSSEDIVALIEPGKVNVIDLGPLDEGQMKLVVAKFLEKVFETRMDYEKARKRLDYLRTAYSSNISAVSDEINELEEFLRGVEKNYPALAEPVMVIVEEAHIFAPHGEKGGAVRILGRIAREGRKFGVGLGLVSQRPSRLSEDVLSQTNTKIIMRIVNPNDQQYVVRASEQVSGELMSDIAGLGKGEAVIVGQAISLPALVKIYNFKALGGNYGGEDIGAVERWLERKRRELEEKEKEEMYEEEGIEVDF

Source

organism	Thermococcus kodakarensis
ncbi_taxonomy_id	311400
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	;5'-3' nuclease, encoded next to Rad50 and Mre11 homologs ;
formula_weight	51035.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

MYRLIDRRSVDRIKALLERGYREAESKLAEIEWKPLPKERKQTRVYAVDGSQGKQRLSGTIFYAVSSYAFGNGPAYRLVYTNAMLYNQGISDQIIRLQMETLENKLGYLSAKLGDVDYVMMDGTLTGSLTRPPVYPESVKGLTTIENALGKGKLKELVKKFVSLLDEHYKELEDGLREKGKINGNVILADEKLEEFEEFYKAMKGYKVRDFAGTTPRGIKISRATIDEYLKGRKSAEEIFQELLNEYGEERELSLDDARNAVHVVLGYLEYLYSLEKLLRLNLVYVAKSFYNRKLTQKLGIDIVDVPYLDAYLRKRFGEEIPGYFIITQGGKAISHKMPKVLRETFPLVEHYIEHGVPMAYVRTMKGGVIYLLQSNREVDDDLLSEILWHESNGYFRPLQRAHEGVKIEKKAFEAELKALLNIIKAESPELRVFLKYGRSPLE

Source

organism	Thermococcus kodakarensis
ncbi_taxonomy_id	311400
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	DNA
formula_weight	6219.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

AAAAAAAAAAAAAAAAAAAA

Entity 4 polymer

description	DNA
formula_weight	6038.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

TTTTTTTTTTTTTTTTTTTT

Entity 5 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	8

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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	2.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.30 Å
resolution_method	—
num_particles	256392

fit	/app/data/saxs_computation/x1/9x1m/9x1m.fit
pddf	/app/data/pr_computation/x1/9x1m/9x1m.pr.out
profile	/app/data/saxs_computation/x1/9x1m/9x1m.dat

The cryo-EM structure of HerA-NurA complex with AMPPNP and dsDNA from Thermococcus kodakarensis

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)